| Title: | Transcriptomic Breast Cancer Datasets |
|---|---|
| Description: | A collection of Breast Cancer Transcriptomic Datasets that are part of the MetaGxData package compendium. |
| Authors: | Michael Zon [aut], Deena M.A. Gendoo [aut], Christopher Eeles [ctb], Benjamin Haibe-Kains [aut, cre] |
| Maintainer: | Benjamin Haibe-Kains <[email protected]> |
| License: | Apache License (>= 2) |
| Version: | 1.32.0 |
| Built: | 2026-10-16 11:18:06 UTC |
| Source: | https://github.com/bioc/MetaGxBreast |
ExpressionSet for the CAL Dataset
experimentData(eset):
Experiment data
Experimenter name:
Laboratory:
Contact information: http://www.ncbi.nlm.nih.gov/pubmed/17157792
Title:
URL: http://www.ebi.ac.uk/arrayexpress/experiments/E-TABM-158/
PMIDs: 17157792
No abstract available.
notes:
summary:
Recurrent copy number abnormalities differ between tumor subtypes as defin
ed by gene expression patterns. Accuracy of stratification by outcome can
be improved by combining expression and copy number.
mapping.method:
maxRowVariance
mapping.group:
EntrezGene.ID
preprocessing:
As published by original author.
featureData(eset):
An object of class 'AnnotatedDataFrame'
featureNames: 1007_s_at 1053_at ... AFFX-HUMISGF3A/M97935_MB_at
(21169 total)
varLabels: probeset gene EntrezGene.ID best_probe
varMetadata: labelDescription
assayData: 21169 features, 118 samples
Platform type:
Overall survival time-to-event summary (in years):
Call: survfit(formula = Surv(time, cens) ~ -1)
1 observation deleted due to missingness
n events median 0.95LCL 0.95UCL
117.00 77.00 8.96 8.33 9.71
---------------------------
Available sample meta-data:
---------------------------
sample_name:
Length Class Mode
118 character character
sample_type:
tumor
118
er:
negative positive
43 75
pgr:
negative positive NA's
51 66 1
tumor_size:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
0.300 1.675 2.300 2.729 3.500 7.500 2
N:
0 1
51 67
age_at_initial_pathologic_diagnosis:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
31.00 44.00 51.00 55.06 66.00 88.00 1
grade:
1 2 3 NA's
10 42 61 5
dmfs_days:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
0 767 2059 2094 3336 5183 1
dmfs_status:
norecurrence recurrence NA's
91 26 1
days_to_tumor_recurrence:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
0 767 2059 2094 3336 5183 1
recurrence_status:
norecurrence recurrence NA's
81 36 1
days_to_death:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
47 1117 2234 2347 3504 5183 1
vital_status:
deceased living
77 41
treatment:
chemo.plus.hormono chemotherapy hormonotherapy untreated
25 36 40 14
NA's
3
batch:
CAL
118
uncurated_author_metadata:
Length Class Mode
118 character character
http://www.ebi.ac.uk/arrayexpress/experiments/E-TABM-158/
ExpressionSet for the DFHCC Dataset
experimentData(eset):
Experiment data
Experimenter name:
Laboratory:
Contact information: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2826790/
Title:
URL: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE19615
PMIDs: 20098429
No abstract available.
notes:
summary:
A small number of over-expressed and over-amplified genes were significant
ly associated with early recurrence despite adjuvant therapy. This was ve
rified in independent cohorts.
mapping.method:
maxRowVariance
mapping.group:
EntrezGene.ID
preprocessing:
As published by original author.
featureData(eset):
An object of class 'AnnotatedDataFrame'
featureNames: 1007_s_at 1053_at ... AFFX-HUMISGF3A/M97935_MB_at
(42447 total)
varLabels: probeset gene EntrezGene.ID best_probe
varMetadata: labelDescription
assayData: 42447 features, 115 samples
Platform type:
---------------------------
Available sample meta-data:
---------------------------
sample_name:
Length Class Mode
115 character character
alt_sample_name:
Min. 1st Qu. Median Mean 3rd Qu. Max.
6.0 155.0 230.0 293.3 398.5 828.0
sample_type:
tumor
115
er:
negative positive
45 70
pgr:
negative positive
51 64
her2:
negative positive
79 36
tumor_size:
Min. 1st Qu. Median Mean 3rd Qu. Max.
0.800 1.350 2.100 2.312 2.850 6.500
N:
0 1
62 53
age_at_initial_pathologic_diagnosis:
Min. 1st Qu. Median Mean 3rd Qu. Max.
32.00 45.00 53.00 53.89 60.00 85.00
grade:
1 2 3
23 28 64
dmfs_days:
Min. 1st Qu. Median Mean 3rd Qu. Max.
30 1500 1920 1799 2325 2640
dmfs_status:
norecurrence recurrence
101 14
treatment:
chemo.plus.hormono chemotherapy hormonotherapy untreated
42 38 22 7
NA's
6
batch:
DFHCC
115
uncurated_author_metadata:
Length Class Mode
115 character character
http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE19615
Test the efficacy of treating TNBC with neoadjuvant cisplatin; explore biomarkers to identify predictors of response
experimentData(eset):
Experiment data
Experimenter name:
Laboratory:
Contact information: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2834466/
Title:
URL: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE18864
PMIDs: 20100965
Abstract: A 16 word abstract is available. Use 'abstract' method.
notes:
summary:
A subset of the patients experienced a response induced by cisplatin and b
iomarkers were identified that could predict response to cisplatin.
mapping.method:
maxRowVariance
mapping.group:
EntrezGene.ID
preprocessing:
As published by original author.
featureData(eset):
An object of class 'AnnotatedDataFrame'
featureNames: 1007_s_at 1053_at ... AFFX-HUMISGF3A/M97935_MB_at
(42447 total)
varLabels: probeset gene EntrezGene.ID best_probe
varMetadata: labelDescription
assayData: 42447 features, 84 samples
Platform type:
---------------------------
Available sample meta-data:
---------------------------
sample_name:
Length Class Mode
84 character character
unique_patient_ID:
Length Class Mode
84 character character
sample_type:
tumor
84
er:
negative positive
53 31
pgr:
negative positive
53 31
her2:
negative positive
66 18
age_at_initial_pathologic_diagnosis:
Min. 1st Qu. Median Mean 3rd Qu. Max.
29.00 45.00 53.00 52.89 59.00 85.00
grade:
1 2 3
10 16 58
treatment:
chemotherapy
84
batch:
DFHCC2_CISPLATIN DFHCC2_REFERENCE
24 60
uncurated_author_metadata:
Length Class Mode
84 character character
duplicates:
Length Class Mode
84 character character
http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE18864
ExpressionSet for the DFHCC3 Dataset
experimentData(eset):
Experiment data
Experimenter name:
Laboratory:
Contact information: http://www.ncbi.nlm.nih.gov/pubmed/16473279
Title:
URL: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE3744
PMIDs: 16473279
No abstract available.
notes:
summary:
Basal like cancerse_often lack an inactivated X chromosome.e_Other markers
found were duplication of the active X chromosome ande_nonheterochromatin
ized X chromosomal DNA. A small subset of X chromosomal genes were overexp
ressed. These abnormalities are thought to led to the pathogenesis of basa
l like cancers.
mapping.method:
maxRowVariance
mapping.group:
EntrezGene.ID
preprocessing:
As published by original author.
featureData(eset):
An object of class 'AnnotatedDataFrame'
featureNames: 1007_s_at 1053_at ... AFFX-HUMISGF3A/M97935_MB_at
(42447 total)
varLabels: probeset gene EntrezGene.ID best_probe
varMetadata: labelDescription
assayData: 42447 features, 40 samples
Platform type:
---------------------------
Available sample meta-data:
---------------------------
sample_name:
Length Class Mode
40 character character
alt_sample_name:
Length Class Mode
40 character character
sample_type:
tumor
40
batch:
DFHCC3
40
uncurated_author_metadata:
Length Class Mode
40 character character
http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE3744
ExpressionSet for the DUKE Dataset
experimentData(eset):
Experiment data
Experimenter name:
Laboratory:
Contact information: http://www.ncbi.nlm.nih.gov/pubmed/16273092
Title:
URL: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=gse3143
PMIDs: 16273092
No abstract available.
notes:
summary:
It was shown that the activatione_status of several oncogenic pathways can
bee_identified by gene expression signatures. These gene signatures ident
ify deregulation of pathways, associations with clinically relevant outcom
es, and characteristics of specific cancers and tumor subtypes.
mapping.method:
maxRowVariance
mapping.group:
EntrezGene.ID
preprocessing:
As published by original author.
featureData(eset):
An object of class 'AnnotatedDataFrame'
featureNames: 1000_at 1001_at ... AFFX-MurIL4_at (12085 total)
varLabels: probeset gene EntrezGene.ID best_probe
varMetadata: labelDescription
assayData: 12085 features, 171 samples
Platform type:
Overall survival time-to-event summary (in years):
Call: survfit(formula = Surv(time, cens) ~ -1)
1 observation deleted due to missingness
n events median 0.95LCL 0.95UCL
170.00 43.00 9.01 6.22 NA
---------------------------
Available sample meta-data:
---------------------------
sample_name:
Length Class Mode
171 character character
alt_sample_name:
Length Class Mode
171 character character
sample_type:
tumor
171
er:
negative positive
57 114
pgr:
negative positive NA's
23 65 83
tumor_size:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
0.20 1.80 2.30 2.74 3.50 8.50 83
N:
0 1 NA's
53 36 82
days_to_death:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
171.0 417.0 957.5 1235.0 1852.0 4069.0 1
vital_status:
deceased living NA's
43 127 1
batch:
DUKE
171
uncurated_author_metadata:
Length Class Mode
171 character character
duplicates:
DUKE.DUKE_T00.622 DUKE.DUKE_T01.052 DUKE.DUKE_T01.522 DUKE.DUKE_T01.534
1 1 1 1
NA's
167
http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=gse3143
Predicting response with gene signature
experimentData(eset):
Experiment data
Experimenter name:
Laboratory:
Contact information: http://www.ncbi.nlm.nih.gov/pubmed/18024211
Title:
URL: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=gse6861
PMIDs: 18024211
Abstract: A 5 word abstract is available. Use 'abstract' method.
notes:
summary:
Retraction in Lancet Feb 2011 (21277543); Regimen specific signatures were
able to predict pathological complete response. Selecting patients with t
hese gene signataures could increase the proportion of patients with pCR t
han by basing clinical decisions on clinical factors.
mapping.method:
maxRowVariance
mapping.group:
EntrezGene.ID
preprocessing:
As published by original author.
featureData(eset):
An object of class 'AnnotatedDataFrame'
featureNames: 1053_3p_at 117_3p_at ... X79510cds_3p_s_at (45490
total)
varLabels: probeset gene EntrezGene.ID best_probe
varMetadata: labelDescription
assayData: 45490 features, 160 samples
Platform type:
---------------------------
Available sample meta-data:
---------------------------
sample_name:
Length Class Mode
160 character character
alt_sample_name:
Length Class Mode
160 character character
sample_type:
tumor
160
er:
negative positive
123 37
pgr:
negative positive NA's
133 25 2
N:
0 1 NA's
58 95 7
age_at_initial_pathologic_diagnosis:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
26.00 43.00 49.00 49.41 56.00 70.00 35
grade:
1 2 3 NA's
2 37 70 51
treatment:
chemotherapy
160
batch:
DUKE2
160
uncurated_author_metadata:
Length Class Mode
160 character character
http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=gse6861
ExpressionSet for the EMC2 Dataset
experimentData(eset):
Experiment data
Experimenter name:
Laboratory:
Contact information: http://www.ncbi.nlm.nih.gov/pubmed/19421193
Title:
URL: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=gse12276
PMIDs: 19421193
No abstract available.
notes:
summary:
Genes were identified that may increase the ability of breast cancer cells
to infiltrate the blood-brain barrier.
mapping.method:
maxRowVariance
mapping.group:
EntrezGene.ID
preprocessing:
As published by original author.
featureData(eset):
An object of class 'AnnotatedDataFrame'
featureNames: 1007_s_at 1053_at ... AFFX-HUMISGF3A/M97935_MB_at
(42447 total)
varLabels: probeset gene EntrezGene.ID best_probe
varMetadata: labelDescription
assayData: 42447 features, 204 samples
Platform type:
---------------------------
Available sample meta-data:
---------------------------
sample_name:
Length Class Mode
204 character character
alt_sample_name:
Min. 1st Qu. Median Mean 3rd Qu. Max.
1.00 51.75 102.50 102.50 153.20 204.00
sample_type:
tumor
204
N:
0 NA's
48 156
dmfs_days:
Min. 1st Qu. Median Mean 3rd Qu. Max.
0 335 640 799 1098 3507
dmfs_status:
norecurrence recurrence
19 185
treatment:
chemotherapy untreated
156 48
batch:
EMC2
204
uncurated_author_metadata:
Length Class Mode
204 character character
http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=gse12276
ExpressionSet for the EORTC10994 Dataset
experimentData(eset):
Experiment data
Experimenter name:
Laboratory:
Contact information: http://www.ncbi.nlm.nih.gov/pubmed/?term=15897907
Title:
URL: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE1561
PMIDs: 15897907
No abstract available.
notes:
summary:
The tumors with an apocrine gene expression profile had strong histologica
l apocrine features. These tumors were androgen receptor positive and were
all ER negative, creating further classifications of tumor cells based on
steroid receptor activity- luminal which are ER and AR positive, basal th
at are ER and AR negative, and molecular apocrine that are ER negative and
AR positive.
mapping.method:
maxRowVariance
mapping.group:
EntrezGene.ID
preprocessing:
As published by original author.
featureData(eset):
An object of class 'AnnotatedDataFrame'
featureNames: 1007_s_at 1053_at ... AFFX-HUMISGF3A/M97935_MB_at
(20967 total)
varLabels: probeset gene EntrezGene.ID best_probe
varMetadata: labelDescription
assayData: 20967 features, 49 samples
Platform type:
---------------------------
Available sample meta-data:
---------------------------
sample_name:
Length Class Mode
49 character character
alt_sample_name:
Length Class Mode
49 character character
sample_type:
tumor
49
er:
negative positive
22 27
pgr:
negative positive NA's
29 18 2
tumor_size:
1 2 3 4
4 23 14 8
N:
0 1
19 30
grade:
1 2 3 NA's
4 22 20 3
batch:
EORTC10994
49
uncurated_author_metadata:
Length Class Mode
49 character character
http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE1561
ExpressionSet for the EXPO Dataset
experimentData(eset):
Experiment data
Experimenter name:
Laboratory:
Contact information:
Title:
URL: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE2109
PMIDs:
No abstract available.
notes:
summary:
N/A
mapping.method:
maxRowVariance
mapping.group:
EntrezGene.ID
preprocessing:
As published by original author.
featureData(eset):
An object of class 'AnnotatedDataFrame'
featureNames: 1007_s_at 1053_at ... AFFX-HUMISGF3A/M97935_MB_at
(42447 total)
varLabels: probeset gene EntrezGene.ID best_probe
varMetadata: labelDescription
assayData: 42447 features, 353 samples
Platform type:
---------------------------
Available sample meta-data:
---------------------------
sample_name:
Length Class Mode
353 character character
alt_sample_name:
Min. 1st Qu. Median Mean 3rd Qu. Max.
1005 21640 101100 134700 215900 486200
sample_type:
tumor
353
er:
negative positive NA's
85 161 107
pgr:
negative positive NA's
114 129 110
her2:
negative positive NA's
166 61 126
age_at_initial_pathologic_diagnosis:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
25.00 45.00 55.00 59.44 67.50 95.00 1
grade:
1 2 3 NA's
32 114 151 56
batch:
EXPO
353
uncurated_author_metadata:
Length Class Mode
353 character character
duplicates:
EXPO.EXPO_GSM53027 EXPO.EXPO_GSM53059 NA's
1 1 351
http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE2109
ExpressionSet for the FNCLCC Dataset
experimentData(eset):
Experiment data
Experimenter name:
Laboratory:
Contact information: http://www.ncbi.nlm.nih.gov/pubmed/?term=17659439
Title:
URL: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE7017
PMIDs: 17659439
No abstract available.
notes:
summary:
A potentially more powerful clinicogenomic model was created by combining
a subset of relevant genes from an already published gene expression signa
ture and a commonly used clinical prognostic model (NPI). The genes in thi
s model are known to have a role in breast cancer, carcinogenesis, or chem
otherapy resistance.
mapping.method:
maxRowVariance
mapping.group:
EntrezGene.ID
preprocessing:
As published by original author.
featureData(eset):
An object of class 'AnnotatedDataFrame'
featureNames: UMGC_00005 UMGC_00007 ... UMGC_09018 (6064 total)
varLabels: probeset gene EntrezGene.ID best_probe
varMetadata: labelDescription
assayData: 6064 features, 150 samples
Platform type:
---------------------------
Available sample meta-data:
---------------------------
sample_name:
Length Class Mode
150 character character
alt_sample_name:
Length Class Mode
150 character character
sample_type:
tumor
150
N:
1
150
treatment:
chemotherapy
150
batch:
FNCLCC
150
uncurated_author_metadata:
Length Class Mode
150 character character
http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE7017
ExpressionSet for the GSE25066 Dataset
experimentData(eset):
Experiment data
Experimenter name:
Laboratory:
Contact information:
Title:
URL: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE25066
PMIDs: 21558518
No abstract available.
notes:
summary:
mapping.method:
maxRowVariance
mapping.group:
EntrezGene.ID
preprocessing:
As published by original author.
featureData(eset):
An object of class 'AnnotatedDataFrame'
featureNames: 1007_s_at 1053_at ... AFFX-HUMISGF3A/M97935_MB_at
(20967 total)
varLabels: probeset gene EntrezGene.ID best_probe
varMetadata: labelDescription
assayData: 20967 features, 508 samples
Platform type:
---------------------------
Available sample meta-data:
---------------------------
sample_name:
Length Class Mode
508 character character
alt_sample_name:
Length Class Mode
508 character character
sample_type:
tumor
508
er:
negative positive NA's
205 297 6
pgr:
negative positive NA's
258 243 7
her2:
negative positive NA's
485 6 17
T:
T0 T1 T2 T3 T4
3 30 255 145 75
N:
0 1
157 351
age_at_initial_pathologic_diagnosis:
Min. 1st Qu. Median Mean 3rd Qu. Max.
24.0 42.0 49.0 49.8 58.0 75.0
grade:
1 2 3 4 NA's
32 180 259 15 22
dmfs_days:
Min. 1st Qu. Median Mean 3rd Qu. Max.
0.0 636.5 999.9 1088.0 1500.0 2717.0
dmfs_status:
norecurrence recurrence
397 111
batch:
GSE25066
508
uncurated_author_metadata:
Length Class Mode
508 character character
chemosensitivity_prediction:
Rx Insensitive Rx Sensitive
339 169
GGI_prediction:
High Low
336 172
PAM50_prediction:
Basal Her2 LumA LumB Normal
189 37 160 78 44
dlda30_prediction:
pCR RD
196 312
RCB_prediction:
RCB-0/I RCB-II/III
230 278
http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE25066
ExpressionSet for the GSE32646 Dataset
experimentData(eset):
Experiment data
Experimenter name:
Laboratory:
Contact information:
Title:
URL: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE32646
PMIDs: 22320227
No abstract available.
notes:
summary:
mapping.method:
maxRowVariance
mapping.group:
EntrezGene.ID
preprocessing:
As published by original author.
featureData(eset):
An object of class 'AnnotatedDataFrame'
featureNames: 1007_s_at 1053_at ... 91952_at (42437 total)
varLabels: probeset gene EntrezGene.ID best_probe
varMetadata: labelDescription
assayData: 42437 features, 115 samples
Platform type:
---------------------------
Available sample meta-data:
---------------------------
sample_name:
Length Class Mode
115 character character
sample_type:
tumor
115
er:
negative positive
44 71
pgr:
negative positive
70 45
her2:
negative positive
81 34
T:
1 2 3 4
5 87 18 5
N:
0 1
32 83
age_at_initial_pathologic_diagnosis:
Min. 1st Qu. Median Mean 3rd Qu. Max.
27.00 45.00 51.00 51.49 59.00 73.00
grade:
1 2 3
16 78 21
batch:
GSE32646
115
uncurated_author_metadata:
Length Class Mode
115 character character
http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE32646
ExpressionSet for the GSE48091 Dataset
experimentData(eset):
Experiment data
Experimenter name:
Laboratory:
Contact information:
Title:
URL: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE48091
PMIDs: 26077471
No abstract available.
notes:
summary:
mapping.method:
maxRowVariance
mapping.group:
EntrezGene.ID
preprocessing:
As published by original author.
featureData(eset):
An object of class 'AnnotatedDataFrame'
featureNames: 100121619_TGI_at 100121620_TGI_at ... 100314044_TGI_at
(23246 total)
varLabels: probeset gene EntrezGene.ID best_probe
varMetadata: labelDescription
assayData: 23246 features, 623 samples
Platform type:
---------------------------
Available sample meta-data:
---------------------------
sample_name:
Length Class Mode
623 character character
sample_type:
tumor
623
batch:
GSE48091
623
uncurated_author_metadata:
Length Class Mode
623 character character
http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE48091
ExpressionSet for the GSE58644 Dataset
experimentData(eset):
Experiment data
Experimenter name:
Laboratory:
Contact information:
Title:
URL: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE58644
PMIDs: 25284793
No abstract available.
notes:
summary:
mapping.method:
maxRowVariance
mapping.group:
EntrezGene.ID
preprocessing:
As published by original author.
featureData(eset):
An object of class 'AnnotatedDataFrame'
featureNames: 7896756 7896759 ... 8180179 (21462 total)
varLabels: probeset gene EntrezGene.ID best_probe
varMetadata: labelDescription
assayData: 21462 features, 321 samples
Platform type:
---------------------------
Available sample meta-data:
---------------------------
sample_name:
Length Class Mode
321 character character
alt_sample_name:
Length Class Mode
321 character character
sample_type:
tumor
321
er:
negative positive NA's
70 250 1
her2:
negative positive NA's
256 58 7
tumor_size:
Min. 1st Qu. Median Mean 3rd Qu. Max.
0.600 1.600 2.100 2.354 2.600 15.000
T:
1 2 3 4 NA's
43 59 13 1 205
N:
0 1 NA's
138 151 32
age_at_initial_pathologic_diagnosis:
Min. 1st Qu. Median Mean 3rd Qu. Max.
29.00 49.00 58.00 58.82 68.00 93.00
grade:
1 2 3 NA's
26 135 159 1
dmfs_status:
norecurrence recurrence
295 26
dmfs_days:
Min. 1st Qu. Median Mean 3rd Qu. Max.
0 9496 17900 21620 33600 52590
treatment:
chemo.plus.hormono chemotherapy hormonotherapy untreated
91 29 66 10
NA's
125
chemo:
0 1 NA's
105 123 93
tamoxifen:
0 1 NA's
39 157 125
herceptin:
0 1 NA's
190 12 119
batch:
GSE58644
321
uncurated_author_metadata:
Length Class Mode
321 character character
duplicates:
Length Class Mode
321 character character
http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE58644
ExpressionSet for the HLP Dataset
experimentData(eset):
Experiment data
Experimenter name:
Laboratory:
Contact information: http://www.ncbi.nlm.nih.gov/pubmed/?term=19688261
Title:
URL: http://www.ebi.ac.uk/arrayexpress/experiments/E-TABM-543/
PMIDs: 19688261
No abstract available.
notes:
summary:
The results show evidence of different patterns of genetic aberrations in
distinct molecular subtypes of breast cancer. Patterns of copy number aber
rations may drive biological phenomena characteristic to each subtype.
mapping.method:
maxRowVariance
mapping.group:
EntrezGene.ID
preprocessing:
As published by original author.
featureData(eset):
An object of class 'AnnotatedDataFrame'
featureNames: 9g8cQB1TZtuiix.ulU fJUdX0IAn_P9VLTgJU ...
xopB7pPn18FJ067uDs (26536 total)
varLabels: probeset gene EntrezGene.ID best_probe
varMetadata: labelDescription
assayData: 26536 features, 53 samples
Platform type:
---------------------------
Available sample meta-data:
---------------------------
sample_name:
Length Class Mode
53 character character
alt_sample_name:
Length Class Mode
53 character character
sample_type:
tumor
53
er:
negative positive
28 25
pgr:
negative positive
33 20
her2:
negative positive
40 13
tumor_size:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
1.200 1.800 2.450 2.648 3.000 8.000 5
N:
0 1 NA's
27 25 1
age_at_initial_pathologic_diagnosis:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
30.00 47.50 53.50 54.96 64.25 81.00 5
grade:
3
53
batch:
HLP
53
uncurated_author_metadata:
Length Class Mode
53 character character
http://www.ebi.ac.uk/arrayexpress/experiments/E-TABM-543/
ExpressionSet for the IRB Dataset
experimentData(eset):
Experiment data
Experimenter name:
Laboratory:
Contact information: http://www.ncbi.nlm.nih.gov/pubmed/18297396
Title:
URL: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE5460
PMIDs: 18297396
No abstract available.
notes:
summary:
mapping.method:
maxRowVariance
mapping.group:
EntrezGene.ID
preprocessing:
As published by original author.
featureData(eset):
An object of class 'AnnotatedDataFrame'
featureNames: 1007_s_at 1053_at ... AFFX-HUMISGF3A/M97935_MB_at
(42447 total)
varLabels: probeset gene EntrezGene.ID best_probe
varMetadata: labelDescription
assayData: 42447 features, 129 samples
Platform type:
---------------------------
Available sample meta-data:
---------------------------
sample_name:
Length Class Mode
129 character character
alt_sample_name:
Length Class Mode
129 character character
sample_type:
tumor
129
er:
negative positive
53 76
her2:
negative positive
98 31
tumor_size:
Min. 1st Qu. Median Mean 3rd Qu. Max.
0.800 1.500 2.200 2.488 3.000 8.500
N:
0 1
64 65
grade:
1 2 3
27 32 70
treatment:
untreated
129
batch:
IRB
129
uncurated_author_metadata:
Length Class Mode
129 character character
http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE5460
link does not work, in progress8
experimentData(eset):
Experiment data
Experimenter name:
Laboratory:
Contact information: http://www.ncbi.nlm.nih.gov/pubmed/12747878
Title:
URL: Unavailable
PMIDs: 12747878
Abstract: A 6 word abstract is available. Use 'abstract' method.
notes:
summary:
A new gene signature was used to accurately predict 90
n the study.
mapping.method:
maxRowVariance
mapping.group:
EntrezGene.ID
preprocessing:
As published by original author.
featureData(eset):
An object of class 'AnnotatedDataFrame'
featureNames: 1007_s_at 1053_at ... AFFX-HUMISGF3A/M97935_MB_at (280
total)
varLabels: probeset gene EntrezGene.ID best_probe
varMetadata: labelDescription
assayData: 280 features, 88 samples
Platform type:
---------------------------
Available sample meta-data:
---------------------------
sample_name:
Length Class Mode
88 character character
alt_sample_name:
Length Class Mode
88 character character
sample_type:
tumor
88
er:
negative positive
15 73
pgr:
negative positive
23 65
tumor_size:
Min. 1st Qu. Median Mean 3rd Qu. Max.
0.20 1.80 2.30 2.74 3.50 8.50
N:
0 1
19 69
treatment:
chemotherapy untreated
61 27
batch:
KOO
88
uncurated_author_metadata:
Length Class Mode
88 character character
duplicates:
Length Class Mode
88 character character
Unavailable
ExpressionSet for the LUND Dataset
experimentData(eset):
Experiment data
Experimenter name:
Laboratory:
Contact information: http://www.ncbi.nlm.nih.gov/pubmed/?term=18430221
Title:
URL: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE31863
PMIDs: 18430221
No abstract available.
notes:
summary:
A significant difference was found between the ER positive subgroup and ER
negative subgroup in the gene expression profiles.
mapping.method:
maxRowVariance
mapping.group:
EntrezGene.ID
preprocessing:
As published by original author.
featureData(eset):
An object of class 'AnnotatedDataFrame'
featureNames: H200006618 H200006808 ... H300022925 (11154 total)
varLabels: probeset gene EntrezGene.ID best_probe
varMetadata: labelDescription
assayData: 11154 features, 143 samples
Platform type:
---------------------------
Available sample meta-data:
---------------------------
sample_name:
Length Class Mode
143 character character
alt_sample_name:
Length Class Mode
143 character character
sample_type:
tumor
143
er:
negative positive
29 114
pgr:
negative positive NA's
47 88 8
tumor_size:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
0.200 1.100 1.500 1.486 1.800 4.000 2
N:
0
143
age_at_initial_pathologic_diagnosis:
Min. 1st Qu. Median Mean 3rd Qu. Max.
27.00 47.50 56.00 54.76 63.00 73.00
batch:
LUNDS1 LUNDS2 LUNDS3 LUNDS4
30 47 22 44
uncurated_author_metadata:
Length Class Mode
143 character character
http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE31863
ExpressionSet for the LUND2 Dataset
experimentData(eset):
Experiment data
Experimenter name:
Laboratory:
Contact information: http://www.ncbi.nlm.nih.gov/pubmed/?term=17452630
Title:
URL: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE5325
PMIDs: 17452630
No abstract available.
notes:
summary:
Microarray signature was able to show PTEN mRNA losse_when IHC was unable,
even though tumors exhibited PTEN loss behavior. Stathmim was an accurate
IHC marker of the signature and had prognostic significance.
mapping.method:
maxRowVariance
mapping.group:
EntrezGene.ID
preprocessing:
As published by original author.
featureData(eset):
An object of class 'AnnotatedDataFrame'
featureNames: 1 2 ... 27648 (22008 total)
varLabels: probeset gene EntrezGene.ID best_probe
varMetadata: labelDescription
assayData: 22008 features, 105 samples
Platform type:
---------------------------
Available sample meta-data:
---------------------------
sample_name:
Length Class Mode
105 character character
alt_sample_name:
Length Class Mode
105 character character
sample_type:
tumor
105
er:
negative positive
60 45
treatment:
hormonotherapy
105
batch:
LUND2
105
uncurated_author_metadata:
Length Class Mode
105 character character
http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE5325
ExpressionSet for the MAINZ Dataset
experimentData(eset):
Experiment data
Experimenter name:
Laboratory:
Contact information: http://www.ncbi.nlm.nih.gov/pubmed/?term=18593943
Title:
URL: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE11121
PMIDs: 18593943
No abstract available.
notes:
summary:
Poor prognosis is noted in tumors with low ER expression, showing the high
est level of proliferative activity. In some tumors with highly expressed
B-cell or T-cell metagenes, metastases rarely occurred, even with high pro
liferation and low ER expression.
mapping.method:
maxRowVariance
mapping.group:
EntrezGene.ID
preprocessing:
As published by original author.
featureData(eset):
An object of class 'AnnotatedDataFrame'
featureNames: 1007_s_at 1053_at ... AFFX-HUMISGF3A/M97935_MB_at
(20967 total)
varLabels: probeset gene EntrezGene.ID best_probe
varMetadata: labelDescription
assayData: 20967 features, 200 samples
Platform type:
---------------------------
Available sample meta-data:
---------------------------
sample_name:
Length Class Mode
200 character character
alt_sample_name:
Length Class Mode
200 character character
sample_type:
tumor
200
er:
negative positive
38 162
tumor_size:
Min. 1st Qu. Median Mean 3rd Qu. Max.
0.100 1.500 2.000 2.070 2.425 6.000
N:
0
200
age_at_initial_pathologic_diagnosis:
Min. 1st Qu. Median Mean 3rd Qu. Max.
25.00 50.00 60.00 59.98 69.00 90.00
grade:
1 2 3
29 136 35
dmfs_days:
Min. 1st Qu. Median Mean 3rd Qu. Max.
30 1905 2715 2816 3855 7200
dmfs_status:
norecurrence recurrence
154 46
treatment:
untreated
200
batch:
MAINZ
200
uncurated_author_metadata:
Length Class Mode
200 character character
http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE11121
ExpressionSet for the MAQC2 Dataset
experimentData(eset):
Experiment data
Experimenter name:
Laboratory:
Contact information: http://www.ncbi.nlm.nih.gov/pubmed/?term=20064235
Title:
URL: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE20194
PMIDs: 20064235
No abstract available.
notes:
summary:
It is possible to build multi-gene classifiers of clinical outcome. Predic
tion accuracy depends on training sample size and classification difficult
y.
mapping.method:
maxRowVariance
mapping.group:
EntrezGene.ID
preprocessing:
As published by original author.
featureData(eset):
An object of class 'AnnotatedDataFrame'
featureNames: 1007_s_at 1053_at ... AFFX-HUMISGF3A/M97935_MB_at
(20967 total)
varLabels: probeset gene EntrezGene.ID best_probe
varMetadata: labelDescription
assayData: 20967 features, 230 samples
Platform type:
---------------------------
Available sample meta-data:
---------------------------
sample_name:
Length Class Mode
230 character character
alt_sample_name:
Length Class Mode
230 character character
sample_type:
tumor
230
er:
negative positive
89 141
pgr:
negative positive
126 104
her2:
negative positive
190 40
N:
0 1
66 164
age_at_initial_pathologic_diagnosis:
Min. 1st Qu. Median Mean 3rd Qu. Max.
26.00 45.00 51.00 52.02 59.00 79.00
grade:
1 2 3
13 94 123
treatment:
chemotherapy
230
batch:
MAQC2
230
uncurated_author_metadata:
Length Class Mode
230 character character
http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE20194
ExpressionSet for the MCCC Dataset
experimentData(eset):
Experiment data
Experimenter name:
Laboratory:
Contact information: http://www.ncbi.nlm.nih.gov/pubmed/?term=19960244
Title:
URL: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE19177
PMIDs: 19960244
No abstract available.
notes:
summary:
Overall, expression and copy number profiling of familial tumors have show
n that the tumors show molecular heterogeneity similar to sporadic tumors
and are defined by their molecular subtypes rather than BRCA1 or BRCA2 ger
mline mutation status.
mapping.method:
maxRowVariance
mapping.group:
EntrezGene.ID
preprocessing:
As published by original author.
featureData(eset):
An object of class 'AnnotatedDataFrame'
featureNames: probe_10017 probe_10021 ... probe_7650767 (19048 total)
varLabels: probeset gene EntrezGene.ID best_probe
varMetadata: labelDescription
assayData: 19048 features, 75 samples
Platform type:
---------------------------
Available sample meta-data:
---------------------------
sample_name:
Length Class Mode
75 character character
sample_type:
tumor
75
batch:
MCCC
75
uncurated_author_metadata:
Length Class Mode
75 character character
http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE19177
ExpressionSet for the MDA4 Dataset
experimentData(eset):
Experiment data
Experimenter name:
Laboratory:
Contact information: http://www.ncbi.nlm.nih.gov/pubmed/?term=16896004
Title:
URL: http://bioinformatics.mdanderson.org/pubdata.html
PMIDs: 16896004
No abstract available.
notes:
summary:
The developed 30-probe set has high sensitivity and negative predictive va
lue, accurately identifying 12 out of 13 patients with pCR and 27 out of 2
8 patients with residual disease.
mapping.method:
maxRowVariance
mapping.group:
EntrezGene.ID
preprocessing:
As published by original author.
featureData(eset):
An object of class 'AnnotatedDataFrame'
featureNames: 1007_s_at 1053_at ... AFFX-HUMISGF3A/M97935_MB_at
(21169 total)
varLabels: probeset gene EntrezGene.ID best_probe
varMetadata: labelDescription
assayData: 21169 features, 129 samples
Platform type:
---------------------------
Available sample meta-data:
---------------------------
sample_name:
Length Class Mode
129 character character
unique_patient_ID:
Length Class Mode
129 character character
sample_type:
tumor
129
er:
negative positive NA's
48 79 2
pgr:
negative positive NA's
73 54 2
her2:
negative positive
114 15
tumor_size:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
0.000 0.500 1.800 2.162 3.000 10.000 8
N:
0 1 NA's
59 62 8
age_at_initial_pathologic_diagnosis:
Min. 1st Qu. Median Mean 3rd Qu. Max.
28.00 43.00 51.00 51.43 61.00 73.00
treatment:
chemotherapy
129
batch:
MDA4
129
uncurated_author_metadata:
Length Class Mode
129 character character
duplicates:
MDA4.MDA4_M207 MDA4.MDA4_M400 NA's
1 1 127
http://bioinformatics.mdanderson.org/pubdata.html
ExpressionSet for the METABRIC Dataset
experimentData(eset):
Experiment data
Experimenter name:
Laboratory:
Contact information: http://www.ncbi.nlm.nih.gov/pubmed/22522925
Title:
URL: https://www.ebi.ac.uk/ega/studies/EGAS00000000083
PMIDs: 22522925
No abstract available.
notes:
summary:
mapping.method:
maxRowVariance
mapping.group:
EntrezGene.ID
preprocessing:
As published by original author.
featureData(eset):
An object of class 'AnnotatedDataFrame'
featureNames: ILMN_1802380 ILMN_1736104 ... ILMN_1709472 (36155
total)
varLabels: probeset gene EntrezGene.ID best_probe
varMetadata: labelDescription
assayData: 36155 features, 2136 samples
Platform type:
Overall survival time-to-event summary (in years):
Call: survfit(formula = Surv(time, cens) ~ -1)
165 observations deleted due to missingness
n events median 0.95LCL 0.95UCL
1971.0 891.0 12.3 11.6 13.2
---------------------------
Available sample meta-data:
---------------------------
sample_name:
Length Class Mode
2136 character character
alt_sample_name:
Length Class Mode
2136 character character
sample_type:
healthy tumor
144 1992
er:
negative positive NA's
440 1508 188
her2:
negative positive NA's
676 148 1312
tumor_size:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
0.000 1.700 2.300 2.621 3.000 18.200 164
N:
0 1 NA's
1042 950 144
age_at_initial_pathologic_diagnosis:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
21.93 51.36 61.78 61.13 70.76 96.29 13
grade:
1 2 3 NA's
170 775 957 234
days_to_death:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
3 1498 2632 2948 4357 9218 147
vital_status:
deceased living NA's
891 1081 164
treatment:
chemo.plus.hormono chemotherapy hormonotherapy untreated
196 226 1029 685
batch:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
1.000 1.000 3.000 2.613 3.000 5.000 144
uncurated_author_metadata:
Length Class Mode
2136 character character
duplicates:
Length Class Mode
2136 character character
https://www.ebi.ac.uk/ega/studies/EGAS00000000083
ExpressionSet for the MSK Dataset
experimentData(eset):
Experiment data
Experimenter name:
Laboratory:
Contact information: http://www.ncbi.nlm.nih.gov/pubmed/?term=16049480
Title:
URL: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=gse2603
PMIDs: 16049480
No abstract available.
notes:
summary:
A set of genes were identified that mark and mediate metastasis to the lun
g. Some genes confer growth advantages to both the breast tumor and lung e
nvironment, while others contribute to aggressive growth specifically in t
he lung.
mapping.method:
maxRowVariance
mapping.group:
EntrezGene.ID
preprocessing:
As published by original author.
featureData(eset):
An object of class 'AnnotatedDataFrame'
featureNames: 1007_s_at 1053_at ... AFFX-HUMISGF3A/M97935_MB_at
(20967 total)
varLabels: probeset gene EntrezGene.ID best_probe
varMetadata: labelDescription
assayData: 20967 features, 99 samples
Platform type:
---------------------------
Available sample meta-data:
---------------------------
sample_name:
Length Class Mode
99 character character
alt_sample_name:
Length Class Mode
99 character character
sample_type:
tumor
99
er:
negative positive
42 57
pgr:
negative positive NA's
55 43 1
her2:
positive NA's
85 14
tumor_size:
Min. 1st Qu. Median Mean 3rd Qu. Max.
1.100 2.450 3.200 3.624 4.300 10.000
N:
0 1
34 65
age_at_initial_pathologic_diagnosis:
Min. 1st Qu. Median Mean 3rd Qu. Max.
30.00 46.50 56.00 55.81 63.50 87.00
dmfs_days:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
245 1279 1971 1888 2575 3924 17
dmfs_status:
norecurrence recurrence NA's
55 27 17
batch:
MSK
99
uncurated_author_metadata:
Length Class Mode
99 character character
http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=gse2603
ExpressionSet for the MUG Dataset
experimentData(eset):
Experiment data
Experimenter name:
Laboratory:
Contact information: http://www.ncbi.nlm.nih.gov/pubmed/?term=18592372
Title:
URL: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=gse10510
PMIDs: 18592372
No abstract available.
notes:
summary:
A method was developed to separate tumor cells and their microenvironment
to test the prognostic abilities of the immune system. Results showed that
lymphatic infiltration is beneficial for ER negative patients, but probab
ly not beneficial for ER positive patients.
mapping.method:
maxRowVariance
mapping.group:
EntrezGene.ID
preprocessing:
As published by original author.
featureData(eset):
An object of class 'AnnotatedDataFrame'
featureNames: H200000001 H200000005 ... opHsV04TC000043 (14288 total)
varLabels: probeset gene EntrezGene.ID best_probe
varMetadata: labelDescription
assayData: 14288 features, 152 samples
Platform type:
---------------------------
Available sample meta-data:
---------------------------
sample_name:
Length Class Mode
152 character character
alt_sample_name:
Length Class Mode
152 character character
sample_type:
tumor
152
batch:
MUG
152
uncurated_author_metadata:
Length Class Mode
152 character character
http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=gse10510
ExpressionSet for the NCCS Dataset
experimentData(eset):
Experiment data
Experimenter name:
Laboratory:
Contact information: http://www.ncbi.nlm.nih.gov/pubmed/?term=18636107
Title:
URL: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=gse5364
PMIDs: 18636107
No abstract available.
notes:
summary:
48 genes were identified that displayed highly restricted levels of expres
sion in tumors compared to normal tissues. This was validated in 11 indepe
ndent cohorts of different cancer types.
mapping.method:
maxRowVariance
mapping.group:
EntrezGene.ID
preprocessing:
As published by original author.
featureData(eset):
An object of class 'AnnotatedDataFrame'
featureNames: 1007_s_at 1053_at ... AFFX-HUMISGF3A/M97935_MB_at
(20967 total)
varLabels: probeset gene EntrezGene.ID best_probe
varMetadata: labelDescription
assayData: 20967 features, 183 samples
Platform type:
---------------------------
Available sample meta-data:
---------------------------
sample_name:
Length Class Mode
183 character character
alt_sample_name:
Min. 1st Qu. Median Mean 3rd Qu. Max.
1.0 46.5 92.0 92.0 137.5 183.0
sample_type:
tumor
183
batch:
NCCS
183
uncurated_author_metadata:
Length Class Mode
183 character character
http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=gse5364
ExpressionSet for the NCI Dataset
experimentData(eset):
Experiment data
Experimenter name:
Laboratory:
Contact information: http://www.ncbi.nlm.nih.gov/pubmed/?term=12917485
Title:
URL: Supplemental data from paper
PMIDs: 12917485
No abstract available.
notes:
summary:
Expression patterns were strongly associated with ER status, moderately as
sociated with grade, but not associated with menopausal state, node status
, or tumor size. Genes that were significantly associated with survival we
re identified.
mapping.method:
maxRowVariance
mapping.group:
EntrezGene.ID
preprocessing:
As published by original author.
featureData(eset):
An object of class 'AnnotatedDataFrame'
featureNames: AF106966 AF217974 ... Y12473 (5154 total)
varLabels: probeset gene EntrezGene.ID best_probe
varMetadata: labelDescription
assayData: 5154 features, 99 samples
Platform type:
---------------------------
Available sample meta-data:
---------------------------
sample_name:
Length Class Mode
99 character character
alt_sample_name:
Min. 1st Qu. Median Mean 3rd Qu. Max.
21580 21610 21640 21650 21670 21830
sample_type:
tumor
99
er:
negative positive
34 65
tumor_size:
Min. 1st Qu. Median Mean 3rd Qu. Max.
0.80 1.80 2.50 2.82 3.00 8.00
N:
0 1
46 53
age_at_initial_pathologic_diagnosis:
Min. 1st Qu. Median Mean 3rd Qu. Max.
33.00 49.00 57.00 57.47 64.50 90.00
grade:
1 2 3
16 38 45
days_to_tumor_recurrence:
Min. 1st Qu. Median Mean 3rd Qu. Max.
8 967 2057 1969 2930 4067
recurrence_status:
norecurrence recurrence
54 45
treatment:
chemotherapy hormonotherapy untreated
10 78 11
batch:
NCI
99
uncurated_author_metadata:
Length Class Mode
99 character character
Supplemental data from paper
ExpressionSet for the NKI Dataset
experimentData(eset):
Experiment data
Experimenter name:
Laboratory:
Contact information: http://www.ncbi.nlm.nih.gov/pubmed/?term=12490681; http://www.ncbi.nlm.nih.gov/pubmed/?term=11823860
Title:
URL: Not available
PMIDs: 12490681, 11823860
No abstract available.
notes:
summary:
It was found that the gene expression profile that was studied was more po
werful in predicting outcome of disease in younger patients than using sta
ndard clinical and pathological criteria.
mapping.method:
maxRowVariance
mapping.group:
EntrezGene.ID
preprocessing:
As published by original author.
featureData(eset):
An object of class 'AnnotatedDataFrame'
featureNames: Contig45645_RC Contig44916_RC ... Contig62037_RC (14960
total)
varLabels: probeset gene EntrezGene.ID best_probe
varMetadata: labelDescription
assayData: 14960 features, 337 samples
Platform type:
Overall survival time-to-event summary (in years):
Call: survfit(formula = Surv(time, cens) ~ -1)
42 observations deleted due to missingness
n events median 0.95LCL 0.95UCL
295 79 NA NA NA
---------------------------
Available sample meta-data:
---------------------------
sample_name:
Length Class Mode
337 character character
alt_sample_name:
Min. 1st Qu. Median Mean 3rd Qu. Max.
4.0 123.0 215.0 214.1 312.0 404.0
sample_type:
tumor
337
er:
negative positive
88 249
tumor_size:
Min. 1st Qu. Median Mean 3rd Qu. Max.
0.200 1.500 2.000 2.241 2.800 5.500
N:
0 1
193 144
age_at_initial_pathologic_diagnosis:
Min. 1st Qu. Median Mean 3rd Qu. Max.
26.0 40.0 45.0 44.2 49.0 62.0
grade:
1 2 3
79 109 149
dmfs_days:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
9 1252 2414 2546 3602 6699 18
dmfs_status:
norecurrence recurrence NA's
210 109 18
days_to_tumor_recurrence:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
9 1252 2414 2546 3602 6699 18
recurrence_status:
norecurrence recurrence NA's
210 109 18
days_to_death:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
20 1934 2637 2870 3763 6694 42
vital_status:
deceased living NA's
79 216 42
treatment:
chemotherapy hormonotherapy untreated
90 40 207
batch:
NKI NKI2
117 220
uncurated_author_metadata:
Length Class Mode
337 character character
Not available
ExpressionSet for the PNC Dataset
experimentData(eset):
Experiment data
Experimenter name:
Laboratory:
Contact information: http://www.ncbi.nlm.nih.gov/pubmed/?term=21910250
Title:
URL: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE20711
PMIDs: GSE20711, PMID 21910250
No abstract available.
notes:
summary:
Breast tumors can be further divided than the currently known expression s
ubtypes based on DNA methylation profiles.
mapping.method:
maxRowVariance
mapping.group:
EntrezGene.ID
preprocessing:
As published by original author.
featureData(eset):
An object of class 'AnnotatedDataFrame'
featureNames: 1007_s_at 1053_at ... AFFX-HUMISGF3A/M97935_MB_at
(42447 total)
varLabels: probeset gene EntrezGene.ID best_probe
varMetadata: labelDescription
assayData: 42447 features, 92 samples
Platform type:
Overall survival time-to-event summary (in years):
Call: survfit(formula = Surv(time, cens) ~ -1)
4 observations deleted due to missingness
n events median 0.95LCL 0.95UCL
88.0 25.0 NA 11.3 NA
---------------------------
Available sample meta-data:
---------------------------
sample_name:
Length Class Mode
92 character character
alt_sample_name:
Length Class Mode
92 character character
sample_type:
tumor
92
er:
negative positive NA's
43 45 4
pgr:
negative positive NA's
43 40 9
her2:
negative positive NA's
64 26 2
tumor_size:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
0.900 1.700 2.500 2.758 3.000 10.000 6
N:
0 1 NA's
43 40 9
age_at_initial_pathologic_diagnosis:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
32.16 48.57 53.90 55.97 64.84 82.13 4
grade:
1 2 3 NA's
13 5 70 4
days_to_tumor_recurrence:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
29 967 2216 2122 2931 5139 7
recurrence_status:
norecurrence recurrence NA's
49 36 7
days_to_death:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
318 1940 2372 2525 3043 5139 4
vital_status:
deceased living NA's
25 63 4
batch:
PNC
92
uncurated_author_metadata:
Length Class Mode
92 character character
http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE20711
ExpressionSet for the STK Dataset
experimentData(eset):
Experiment data
Experimenter name:
Laboratory:
Contact information: http://www.ncbi.nlm.nih.gov/pubmed/?term=16280042
Title:
URL: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=gse1456
PMIDs: 16280042
No abstract available.
notes:
summary:
Expression profiling was able to better predict prognosis compared to hist
ological staging.
mapping.method:
maxRowVariance
mapping.group:
EntrezGene.ID
preprocessing:
As published by original author.
featureData(eset):
An object of class 'AnnotatedDataFrame'
featureNames: 1007_s_at 1053_at ... 244889_at (36178 total)
varLabels: probeset gene EntrezGene.ID best_probe
varMetadata: labelDescription
assayData: 36178 features, 159 samples
Platform type:
---------------------------
Available sample meta-data:
---------------------------
sample_name:
Length Class Mode
159 character character
alt_sample_name:
Min. 1st Qu. Median Mean 3rd Qu. Max.
1.0 67.0 136.0 138.3 208.5 277.0
sample_type:
tumor
159
er:
negative positive
29 130
age_at_initial_pathologic_diagnosis:
Min. 1st Qu. Median Mean 3rd Qu. Max.
31.0 48.0 56.0 57.8 68.5 87.0
grade:
1 2 3 NA's
28 58 61 12
days_to_tumor_recurrence:
Min. 1st Qu. Median Mean 3rd Qu. Max.
66 2022 2467 2234 2846 3099
recurrence_status:
norecurrence recurrence
113 46
treatment:
chemotherapy hormonotherapy untreated
89 48 22
batch:
STK
159
uncurated_author_metadata:
Length Class Mode
159 character character
http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=gse1456
ExpressionSet for the STNO2 Dataset
experimentData(eset):
Experiment data
Experimenter name:
Laboratory:
Contact information: http://www.ncbi.nlm.nih.gov/pubmed/?term=12829800
Title:
URL: http://smd.princeton.edu/cgi-bin/publication/viewPublication.pl?pub_no=248
PMIDs: 12829800
No abstract available.
notes:
summary:
Distinct breast cancer subtypes were determined by gene expression profile
s and were validated in other published datasets.
mapping.method:
maxRowVariance
mapping.group:
EntrezGene.ID
preprocessing:
As published by original author.
featureData(eset):
An object of class 'AnnotatedDataFrame'
featureNames: IMAGE:1020315 IMAGE:1030271 ... IMAGE:971399 (3663
total)
varLabels: probeset gene EntrezGene.ID best_probe
varMetadata: labelDescription
assayData: 3663 features, 118 samples
Platform type:
Overall survival time-to-event summary (in years):
Call: survfit(formula = Surv(time, cens) ~ -1)
n events median 0.95LCL 0.95UCL
118.00 46.00 4.67 3.34 NA
---------------------------
Available sample meta-data:
---------------------------
sample_name:
Length Class Mode
118 character character
alt_sample_name:
Length Class Mode
118 character character
sample_type:
tumor
118
er:
negative positive NA's
31 82 5
tumor_size:
1 2 3 4 NA's
6 13 62 32 5
N:
0 1 NA's
34 79 5
age_at_initial_pathologic_diagnosis:
Min. 1st Qu. Median Mean 3rd Qu. Max.
21.00 46.25 58.00 58.47 71.75 85.00
grade:
1 2 3 NA's
11 49 53 5
days_to_tumor_recurrence:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
122.0 396.0 761.0 927.9 1233.0 2800.0 23
recurrence_status:
norecurrence recurrence
58 60
days_to_death:
Min. 1st Qu. Median Mean 3rd Qu. Max.
91 426 898 1019 1392 5722
vital_status:
deceased living
46 72
treatment:
chemotherapy hormonotherapy untreated
23 73 22
batch:
STNO2
118
uncurated_author_metadata:
Length Class Mode
118 character character
http://smd.princeton.edu/cgi-bin/publication/viewPublication.pl?pub_no=248
ExpressionSet for the TCGA Dataset
experimentData(eset):
Experiment data
Experimenter name:
Laboratory:
Contact information: http://www.ncbi.nlm.nih.gov/pubmed/23000897
Title:
URL: http://cancergenome.nih.gov/
PMIDs: 23000897
No abstract available.
notes:
summary:
mapping.method:
maxRowVariance
mapping.group:
EntrezGene.ID
preprocessing:
As published by original author.
featureData(eset):
An object of class 'AnnotatedDataFrame'
featureNames: A1BG A2M ... ARHGAP11A.2 (19504 total)
varLabels: probeset gene EntrezGene.ID best_probe
varMetadata: labelDescription
assayData: 19504 features, 1073 samples
Platform type:
Overall survival time-to-event summary (in years):
Call: survfit(formula = Surv(time, cens) ~ -1)
n events median 0.95LCL 0.95UCL
1073.00 103.00 10.05 8.56 12.05
---------------------------
Available sample meta-data:
---------------------------
sample_name:
Length Class Mode
1073 character character
alt_sample_name:
Length Class Mode
1073 character character
unique_patient_ID:
Length Class Mode
1073 character character
sample_type:
tumor
1073
er:
negative positive NA's
233 790 50
pgr:
negative positive NA's
334 686 53
her2:
negative positive NA's
549 161 363
age_at_initial_pathologic_diagnosis:
Min. 1st Qu. Median Mean 3rd Qu. Max.
26.00 49.00 58.00 58.48 68.00 90.00
days_to_death:
Min. 1st Qu. Median Mean 3rd Qu. Max.
-7.0 137.0 412.0 820.3 1180.0 6796.0
vital_status:
deceased living
103 970
batch:
TCGA
1073
uncurated_author_metadata:
Length Class Mode
1073 character character
http://cancergenome.nih.gov/
ExpressionSet for the TRANSBIG Dataset
experimentData(eset):
Experiment data
Experimenter name:
Laboratory:
Contact information: http://www.ncbi.nlm.nih.gov/pubmed/?term=17545524
Title:
URL: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=gsE7390
PMIDs: 17545524
No abstract available.
notes:
summary:
The 76-gene signature was validated. The results supports the hypothesis t
hat utilizing the gene signature could reduce the number of patients who r
eceive unnecessary adjuvant therapy.
mapping.method:
maxRowVariance
mapping.group:
EntrezGene.ID
preprocessing:
As published by original author.
featureData(eset):
An object of class 'AnnotatedDataFrame'
featureNames: 1007_s_at 1053_at ... AFFX-HUMISGF3A/M97935_MB_at
(20967 total)
varLabels: probeset gene EntrezGene.ID best_probe
varMetadata: labelDescription
assayData: 20967 features, 198 samples
Platform type:
Overall survival time-to-event summary (in years):
Call: survfit(formula = Surv(time, cens) ~ -1)
n events median 0.95LCL 0.95UCL
198.0 56.0 NA 17.1 NA
---------------------------
Available sample meta-data:
---------------------------
sample_name:
Length Class Mode
198 character character
sample_type:
tumor
198
er:
negative positive
64 134
tumor_size:
Min. 1st Qu. Median Mean 3rd Qu. Max.
0.600 1.700 2.000 2.181 2.500 5.000
N:
0
198
age_at_initial_pathologic_diagnosis:
Min. 1st Qu. Median Mean 3rd Qu. Max.
24.00 42.00 46.00 46.39 51.00 60.00
grade:
1 2 3 NA's
30 83 83 2
dmfs_days:
Min. 1st Qu. Median Mean 3rd Qu. Max.
125 2375 4384 3954 5566 9108
dmfs_status:
norecurrence recurrence
147 51
days_to_tumor_recurrence:
Min. 1st Qu. Median Mean 3rd Qu. Max.
121 1528 3534 3399 5130 8711
recurrence_status:
norecurrence recurrence
112 86
days_to_death:
Min. 1st Qu. Median Mean 3rd Qu. Max.
146 2744 4562 4150 5610 9108
vital_status:
deceased living
56 142
treatment:
untreated
198
batch:
VDXGUYU VDXIGRU VDXKIU VDXOXFU VDXRHU
36 50 51 24 37
uncurated_author_metadata:
Length Class Mode
198 character character
http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=gsE7390
ExpressionSet for the UCSF Dataset
experimentData(eset):
Experiment data
Experimenter name:
Laboratory:
Contact information: http://www.ncbi.nlm.nih.gov/pubmed/?term=17428335; http://www.ncbi.nlm.nih.gov/pubmed/?term=14612510
Title:
URL: Not available
PMIDs: 17428335, 14612510
No abstract available.
notes:
summary:
A gene set was identified that correctly predicted outcomes more effective
ly than using histological markers.
mapping.method:
maxRowVariance
mapping.group:
EntrezGene.ID
preprocessing:
As published by original author.
featureData(eset):
An object of class 'AnnotatedDataFrame'
featureNames: probe_1 probe_3 ... probe_10365 (8015 total)
varLabels: probeset gene EntrezGene.ID best_probe
varMetadata: labelDescription
assayData: 8015 features, 162 samples
Platform type:
Overall survival time-to-event summary (in years):
Call: survfit(formula = Surv(time, cens) ~ -1)
29 observations deleted due to missingness
n events median 0.95LCL 0.95UCL
133.00 44.00 11.56 9.25 NA
---------------------------
Available sample meta-data:
---------------------------
sample_name:
Length Class Mode
162 character character
alt_sample_name:
Length Class Mode
162 character character
sample_type:
tumor
162
er:
negative positive NA's
41 101 20
pgr:
negative positive NA's
46 94 22
her2:
negative positive NA's
35 19 108
tumor_size:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
0.000 1.800 2.000 2.682 3.200 11.000 7
N:
0 1 NA's
67 82 13
age_at_initial_pathologic_diagnosis:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
28.00 44.00 53.00 56.61 70.00 88.00 9
grade:
1 2 3 NA's
14 62 74 12
dmfs_days:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
47 897 2040 2084 2992 8267 29
dmfs_status:
norecurrence recurrence
140 22
days_to_tumor_recurrence:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
47 861 1865 1985 2847 8267 29
recurrence_status:
norecurrence recurrence
125 37
days_to_death:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
47 1087 2054 2140 3087 8267 29
vital_status:
deceased living NA's
54 99 9
treatment:
chemo.plus.hormono chemotherapy hormonotherapy untreated
31 38 61 22
NA's
10
batch:
UCSF
162
uncurated_author_metadata:
Length Class Mode
162 character character
Not available
ExpressionSet for the UNC4 Dataset
experimentData(eset):
Experiment data
Experimenter name:
Laboratory:
Contact information: http://www.ncbi.nlm.nih.gov/pubmed/?term=20813035
Title:
URL: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=gse18229
PMIDs: 20813035
No abstract available.
notes:
summary:
Clinically, this subtype is usually triple negative invasive ductal carcin
omas with a poor prognosis. Response to standard of care preoperative chem
otherapy is intermediate between basal-like and luminal tumors. The claudi
n-low subtype most closely resembles the mammary epithelial stem cell.
mapping.method:
maxRowVariance
mapping.group:
EntrezGene.ID
preprocessing:
As published by original author.
featureData(eset):
An object of class 'AnnotatedDataFrame'
featureNames: probe.10 probe.12 ... probe.79701 (5420 total)
varLabels: probeset gene EntrezGene.ID best_probe
varMetadata: labelDescription
assayData: 5420 features, 305 samples
Platform type:
Overall survival time-to-event summary (in years):
Call: survfit(formula = Surv(time, cens) ~ -1)
65 observations deleted due to missingness
n events median 0.95LCL 0.95UCL
240.00 51.00 7.73 6.82 NA
---------------------------
Available sample meta-data:
---------------------------
sample_name:
Length Class Mode
305 character character
sample_type:
tumor
305
er:
negative positive NA's
99 154 52
pgr:
negative positive NA's
126 109 70
her2:
negative positive NA's
203 58 44
tumor_size:
1 1.5 3 6 NA's
60 1 129 43 72
N:
0 1 NA's
126 135 44
age_at_initial_pathologic_diagnosis:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
24.00 46.00 55.00 56.73 68.00 89.00 59
grade:
1 2 3 NA's
25 80 138 62
days_to_tumor_recurrence:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
30.0 450.0 750.0 954.3 1380.0 3540.0 64
recurrence_status:
norecurrence recurrence NA's
170 70 65
days_to_death:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
30 540 885 1104 1590 5190 65
vital_status:
deceased living NA's
51 189 65
batch:
UNC4
305
uncurated_author_metadata:
Length Class Mode
305 character character
duplicates:
KOO.KOO_KF_105 KOO.KOO_T01_514 NA's
1 1 303
http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=gse18229
ExpressionSet for the UNT Dataset
experimentData(eset):
Experiment data
Experimenter name:
Laboratory:
Contact information: http://www.ncbi.nlm.nih.gov/pubmed/?term=16478745; http://www.ncbi.nlm.nih.gov/pubmed/?term=17401012
Title:
URL: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=gse2990
PMIDs: 16478745, 17401012
No abstract available.
notes:
summary:
A gene expression grading index (GGI) was developed. The GGI reclassified
grade 2 patients into two groups with low and high risks of recurrence.
mapping.method:
maxRowVariance
mapping.group:
EntrezGene.ID
preprocessing:
As published by original author.
featureData(eset):
An object of class 'AnnotatedDataFrame'
featureNames: 1007_s_at 1053_at ... 244889_at (36084 total)
varLabels: probeset gene EntrezGene.ID best_probe
varMetadata: labelDescription
assayData: 36084 features, 133 samples
Platform type:
---------------------------
Available sample meta-data:
---------------------------
sample_name:
Length Class Mode
133 character character
alt_sample_name:
Length Class Mode
133 character character
sample_type:
tumor
133
er:
negative positive NA's
40 86 7
pgr:
negative positive NA's
6 56 71
tumor_size:
Min. 1st Qu. Median Mean 3rd Qu. Max.
0.000 1.200 1.900 1.892 2.300 6.000
N:
0
133
age_at_initial_pathologic_diagnosis:
Min. 1st Qu. Median Mean 3rd Qu. Max.
24.00 44.00 53.00 51.79 60.00 73.00
grade:
1 2 3 NA's
32 51 29 21
dmfs_days:
Min. 1st Qu. Median Mean 3rd Qu. Max.
61 1338 2809 2724 4078 5305
dmfs_status:
norecurrence recurrence NA's
97 28 8
days_to_tumor_recurrence:
Min. 1st Qu. Median Mean 3rd Qu. Max.
61 1338 2675 2687 3912 5305
recurrence_status:
norecurrence recurrence NA's
76 49 8
treatment:
untreated
133
batch:
KIU OXFU
64 69
uncurated_author_metadata:
Length Class Mode
133 character character
http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=gse2990
ExpressionSet for the UPP Dataset
experimentData(eset):
Experiment data
Experimenter name:
Laboratory:
Contact information: http://www.ncbi.nlm.nih.gov/pubmed/?term=16141321
Title:
URL: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=gse3494
PMIDs: 16141321
No abstract available.
notes:
summary:
A 32-gene expression signature of p53 was identified that differentiates p
-53 mutant and wild-type tumors. The signature is more effective than sequ
ence-based assessments of p53 in predicting prognosis and therapeutic resp
onse.
mapping.method:
maxRowVariance
mapping.group:
EntrezGene.ID
preprocessing:
As published by original author.
featureData(eset):
An object of class 'AnnotatedDataFrame'
featureNames: 1007_s_at 1053_at ... 244889_at (36178 total)
varLabels: probeset gene EntrezGene.ID best_probe
varMetadata: labelDescription
assayData: 36178 features, 251 samples
Platform type:
---------------------------
Available sample meta-data:
---------------------------
sample_name:
Length Class Mode
251 character character
alt_sample_name:
Length Class Mode
251 character character
sample_type:
tumor
251
er:
negative positive NA's
34 213 4
pgr:
negative positive
61 190
tumor_size:
Min. 1st Qu. Median Mean 3rd Qu. Max.
0.200 1.500 2.000 2.243 2.562 13.000
N:
0 1 NA's
158 84 9
age_at_initial_pathologic_diagnosis:
Min. 1st Qu. Median Mean 3rd Qu. Max.
28.00 52.00 64.00 62.11 72.00 93.00
grade:
1 2 3 NA's
67 128 54 2
days_to_tumor_recurrence:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
30 1870 3711 3007 3985 4654 17
recurrence_status:
norecurrence recurrence NA's
181 55 15
treatment:
hormonotherapy untreated NA's
80 142 29
batch:
UPPT UPPU
80 171
uncurated_author_metadata:
Length Class Mode
251 character character
http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=gse3494
ExpressionSet for the VDX Dataset
experimentData(eset):
Experiment data
Experimenter name:
Laboratory:
Contact information: http://www.ncbi.nlm.nih.gov/pubmed/?term=15721472; http://www.ncbi.nlm.nih.gov/pubmed/?term=17420468
Title:
URL: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=gse2034; http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=gse5327
PMIDs: 15721472, 17420468
No abstract available.
notes:
summary:
15721472: A gene signature was identified that can accurately predict dist
ant metastases in node-negative cases. 17420468: Tumors with a lung metast
atic gene signature were shown to be larger.
mapping.method:
maxRowVariance
mapping.group:
EntrezGene.ID
preprocessing:
As published by original author.
featureData(eset):
An object of class 'AnnotatedDataFrame'
featureNames: 1007_s_at 1053_at ... AFFX-HUMISGF3A/M97935_MB_at
(21169 total)
varLabels: probeset gene EntrezGene.ID best_probe
varMetadata: labelDescription
assayData: 21169 features, 344 samples
Platform type:
---------------------------
Available sample meta-data:
---------------------------
sample_name:
Length Class Mode
344 character character
alt_sample_name:
Min. 1st Qu. Median Mean 3rd Qu. Max.
3.0 122.8 605.5 575.7 836.5 2038.0
sample_type:
tumor
344
er:
negative positive
135 209
tumor_size:
1 2 3 4 NA's
146 132 5 3 58
N:
0
344
age_at_initial_pathologic_diagnosis:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
26.00 44.00 52.00 53.88 63.00 83.00 58
grade:
1 2 3 NA's
7 42 148 147
dmfs_days:
Min. 1st Qu. Median Mean 3rd Qu. Max.
61 1254 2616 2377 3285 5201
dmfs_status:
norecurrence recurrence
226 118
treatment:
untreated
344
batch:
VDX VDXN
286 58
uncurated_author_metadata:
Length Class Mode
344 character character
http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=gse2034; http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=gse5327
The object is a list where each element is a patient ID that is believed to be a duplicate of a patient in another dataset. Patients are designated as duplicated if they have Spearman correlations greater than or equal to 0.98 with other patient expression profiles
A list with 107 elements, each of which is a patient ID.
This function returns breast cancer datasets from the hub and a vector of patients from the datasets that are duplicates based on a spearman correlation > 0.98
loadBreastDatasets( rescale = FALSE, minNumberGenes = 0, minNumberEvents = 0, minSampleSize = 0, keepCommonOnly = FALSE, imputeMissing = FALSE, removeDuplicates = FALSE )loadBreastDatasets( rescale = FALSE, minNumberGenes = 0, minNumberEvents = 0, minSampleSize = 0, keepCommonOnly = FALSE, imputeMissing = FALSE, removeDuplicates = FALSE )
rescale |
apply centering and scaling to the expression sets (default FALSE) |
minNumberGenes |
an integer specifying to remove expression sets with less genes than this number (default 0) |
minNumberEvents |
an integer specifying how man survival events must be in the dataset to keep the dataset (default 0) |
minSampleSize |
an integer specifying the minimum number of patients required in a summarizedExperiment (default 0) |
keepCommonOnly |
remove entrezIDs not common to all datasets (default FALSE) |
imputeMissing |
remove patients from datasets with missing expression values |
removeDuplicates |
remove patients with a Spearman correlation greater than or equal to 0.98 with other patient expression profiles (default TRUE) |
A 'list' with 2 elements. The First element named 'SummarizedExperiment's contains the datasets. The second element named duplicates contains a vector with patient IDs for the duplicate patients (those with Spearman correlation greater than or equal to 0.98 with other patient expression profiles).
This function returns breast cancer datasets from the hub and a vector of patients from the datasets that are most likely duplicates
loadBreastEsets( loadString = "majority", removeDuplicates = TRUE, quantileCutoff = 0, rescale = FALSE, minNumberGenes = 0, minNumberEvents = 0, minSampleSize = 0, removeRetracted = TRUE, removeSubsets = TRUE, keepCommonOnly = FALSE, imputeMissing = FALSE )loadBreastEsets( loadString = "majority", removeDuplicates = TRUE, quantileCutoff = 0, rescale = FALSE, minNumberGenes = 0, minNumberEvents = 0, minSampleSize = 0, removeRetracted = TRUE, removeSubsets = TRUE, keepCommonOnly = FALSE, imputeMissing = FALSE )
loadString |
a character vector specifying which data will be loaded. The default is "majority", which loads in 37 of the 39 datasets. The other option is to provide a character vecotr of the names of the datasets to load. The metabric and tcga datasets areloaded separately as they are very large and doing so will help prevent memory allocation errors for R windows. Furthermore, these datasets are so large that they dominate statistical analyses so it is best that they are analyzed separate of the 37 smaller datasets loaded with the string majority |
removeDuplicates |
remove patients with a Spearman correlation greater than or equal to 0.98 with other patient expression profiles (default TRUE) |
quantileCutoff |
A nueric between 0 and 1 specifying to remove genes with standard deviation below the required quantile (default 0) |
rescale |
apply centering and scaling to the expression sets (default FALSE) |
minNumberGenes |
an integer specifying to remove expression sets with less genes than this number (default 0) |
minNumberEvents |
an integer specifying how man survival events must be in the dataset to keep the dataset (default 0) |
minSampleSize |
an integer specifying the minimum number of patients required in an eset (default 0) |
removeRetracted |
remove datasets from retracted papers (default TRUE, currently just PMID17290060 dataset) |
removeSubsets |
remove datasets that are a subset of other datasets (defeault TRUE, currently just PMID19318476) |
keepCommonOnly |
remove probes not common to all datasets (default FALSE) |
imputeMissing |
remove patients from datasets with missing expression values |
a list with 2 elements. The First element named esets contains the datasets. The second element named duplicates contains a vector with patient IDs for the duplicate patients (those with Spearman correlation greater than or equal to 0.98 with other patient expression profiles).
## Use the default loadString="majority" if you want the 37 smaller datasets esetsAndDups <- loadBreastEsets(loadString = c("CAL", "DFHCC", "DFHCC2", "DFHCC3", "DUKE", "DUKE2", "EMC2"))## Use the default loadString="majority" if you want the 37 smaller datasets esetsAndDups <- loadBreastEsets(loadString = c("CAL", "DFHCC", "DFHCC2", "DFHCC3", "DUKE", "DUKE2", "EMC2"))