| Title: | Various data sets for use with the puma package |
|---|---|
| Description: | This is a simple data package including various data sets derived from the estrogen data for use with the puma (Propagating Uncertainty in Microarray Analysis) package. |
| Authors: | Richard Pearson |
| Maintainer: | Xuejun liu <[email protected]> |
| License: | LGPL |
| Version: | 2.48.0 |
| Built: | 2026-10-10 11:05:15 UTC |
| Source: | https://github.com/bioc/pumadata |
This data is taken from the estrogen package. It was created to be used in the vignette for the puma pacakge. It can be produced using the following code:
library(estrogen)
datadir <- file.path(.find.package("estrogen"),"extdata")
estrogenFilenames <- c("low10-1.cel","low10-2.cel","high10-1.cel","high10-2.cel"
, "low48-1.cel","low48-2.cel","high48-1.cel","high48-2.cel")
affybatch.estrogen <- ReadAffy(
filenames=estrogenFilenames
, celfile.path=datadir
)
pData(affybatch.estrogen) <- data.frame(
"estrogen"=c("absent","absent","present","present"
,"absent","absent","present","present")
, "time.h"=c("10","10","10","10","48","48","48","48")
, row.names=rownames(pData(affybatch.estrogen))
)
data(affybatch.estrogen)data(affybatch.estrogen)
An AffyBatch object containing 8 HG\_U95Av2 arrays, in a 2 x 2 factorial design, with 2 replicates for each combination of factors. The factors are estrogen (absent of present) and time.h (10 or 48).
This data is taken from the estrogen package. It was created to be used in the vignette for the puma pacakge. It can be produced using the following code (note this could take a long time to run):
data(eset_estrogen_mmgmos) eset_estrogen_mmgmos_normd <- PUMAnormalize(eset_estrogen_mmgmos, "median") eset_estrogen_comb <- PUMAcomb(eset_estrogen_mmgmos_normd)
data(eset_estrogen_comb)data(eset_estrogen_comb)
An ExpressionSet object containing the expression levels and standard errors from combining the replicates for each combination of levels of factors from 8 HG\_U95Av2 arrays, in a 2 x 2 factorial design, with 2 replicates for each combination of factors. The factors are estrogen (absent of present) and time.h (10 or 48).
data(eset_estrogen_comb) exprs(eset_estrogen_comb)[1:3,1:3] assayDataElement(eset_estrogen_comb,"se.exprs")[1:3,1:3]data(eset_estrogen_comb) exprs(eset_estrogen_comb)[1:3,1:3] assayDataElement(eset_estrogen_comb,"se.exprs")[1:3,1:3]
This data is taken from the estrogen package. It was created to be used in the vignette for the puma pacakge. It can be produced using the following code (note this could take a long time to run):
data(oligo.estrogen) eset_estrogen_mmgmos <- mmgmos(oligo.estrogen)
data(eset_estrogen_mmgmos)data(eset_estrogen_mmgmos)
An exprReslt object containing expression levels and standard errors for 8 HG\_U95Av2 arrays, in a 2 x 2 factorial design, with 2 replicates for each combination of factors. The factors are estrogen (absent of present) and time.h (10 or 48).
oligo.estrogen
eset_estrogen_rma
data(eset_estrogen_mmgmos) show(eset_estrogen_mmgmos) exprs(eset_estrogen_mmgmos)[1:3,1:3] assayDataElement(eset_estrogen_mmgmos,"se.exprs")[1:3,1:3]data(eset_estrogen_mmgmos) show(eset_estrogen_mmgmos) exprs(eset_estrogen_mmgmos)[1:3,1:3] assayDataElement(eset_estrogen_mmgmos,"se.exprs")[1:3,1:3]
This data is taken from the estrogen package. It was created to be used in the vignette for the puma pacakge. It can be produced using the following code (note this could take a long time to run):
data(oligo.estrogen) eset_estrogen_pmmmgmos <- pmmmgmos(oligo.estrogen)
data(eset_estrogen_pmmmgmos)data(eset_estrogen_pmmmgmos)
An exprReslt object containing expression levels and standard errors for 8 HG\_U95Av2 arrays, in a 2 x 2 factorial design, with 2 replicates for each combination of factors. The factors are estrogen (absent of present) and time.h (10 or 48).
oligo.estrogen
eset_estrogen_rma
data(eset_estrogen_pmmmgmos) show(eset_estrogen_pmmmgmos) exprs(eset_estrogen_pmmmgmos)[1:3,1:3] assayDataElement(eset_estrogen_pmmmgmos,"se.exprs")[1:3,1:3]data(eset_estrogen_pmmmgmos) show(eset_estrogen_pmmmgmos) exprs(eset_estrogen_pmmmgmos)[1:3,1:3] assayDataElement(eset_estrogen_pmmmgmos,"se.exprs")[1:3,1:3]
This data is taken from the estrogen package. It was created to be used in the vignette for the puma pacakge. It can be produced using the following code:
data(oligo.estrogen) eset_estrogen_mmgmos <- rma(oligo.estrogen)
data(eset_estrogen_rma)data(eset_estrogen_rma)
An ExpressionSet object
taining expression levels for 8 HG\_U95Av2 arrays, in
a 2 x 2 factorial design, with 2 replicates for each
combination of factors. The factors are estrogen (absent
of present) and time.h (10 or 48).
oligo.estrogen
eset_estrogen_mmgmos
data(eset_estrogen_rma) show(eset_estrogen_rma) exprs(eset_estrogen_rma)[1:3,1:3] assayDataElement(eset_estrogen_rma,"se.exprs")[1:3,1:3]data(eset_estrogen_rma) show(eset_estrogen_rma) exprs(eset_estrogen_rma)[1:3,1:3] assayDataElement(eset_estrogen_rma,"se.exprs")[1:3,1:3]
This data include the probes location for hta2.0 chips.
data(HTA_Location)data(HTA_Location)
A 1*5118823 matrix including the location for unique probes in HTA_transcript_NO.
Danielle Thierry-Mieg ,Jean Thierry-Mieg. Aceview: a comprehensive cDNA-supported gene and transcripts annotaion. Genome Biology.2006,7(Suppl 1):S12
Manhong Dai, Pinglang Wang,Andrew D. Boyd. (2005) Evolving gene/transcript definitions significantly alter the interpretation of GeneChip data,Nucleic Acid Research 33(20):e175.
This data is the number of probes and the number of transcripts mapped to each gene for hta2.0 chips.
data(HTA_probes_transcripts)data(HTA_probes_transcripts)
A 33394*2 matrix including the number of probes and the number of transcripts mapped to each of 33394 genes for hta20 chips.
Danielle Thierry-Mieg ,Jean Thierry-Mieg. Aceview: a comprehensive cDNA-supported gene and transcripts annotaion Genome Biology.2006,7(Suppl 1):S12
Manhong Dai, Pinglang Wang,Andrew D. Boyd. (2005) Evolving gene/transcript definitions significantly alter the interpretation of GeneChip data,Nucleic Acid Research 33(20):e175.
This data include the names of transcripts mapped to each gene for hta2.0 chips.
data(HTA_transcript_name)data(HTA_transcript_name)
A 225456*1 matrix including 225456 transcript names mapped to genes for hta2.0 chips.
Danielle Thierry-Mieg ,Jean Thierry-Mieg. Aceview: a comprehensive cDNA-supported gene and transcripts annotaion Genome Biology.2006,7(Suppl 1):S12
Manhong Dai, Pinglang Wang,Andrew D. Boyd. (2005) Evolving gene/transcript definitions significantly alter the interpretation of GeneChip data,Nucleic Acid Research 33(20):e175.
This data include the coordinates of probes and the mapped transcripts for hta2.0 chips.
data(HTA_transcript_NO)data(HTA_transcript_NO)
A 20626078*3 matrix including pos_x,pos_y and transcript_no. pos_x and pos_y are respectively X and Y coordinates of probes for hta2.0 chips. Transcript_no is the mapped transcripts for each probe.
Danielle Thierry-Mieg ,Jean Thierry-Mieg. Aceview: a comprehensive cDNA-supported gene and transcripts annotaion Genome Biology.2006,7(Suppl 1):S12
Manhong Dai, Pinglang Wang,Andrew D. Boyd. (2005) Evolving gene/transcript definitions significantly alter the interpretation of GeneChip data,Nucleic Acid Research 33(20):e175.
This data include the probes location for human exon chips.
data(Human_Location)data(Human_Location)
A 1*1565476 matrix including the location for unique probes in Human_transcript_NO.
Risueno A, Fontanillo C, Dinger ME, De Las Rivas J. GATExplorer: genomic and transcriptomic explorer; mapping expression probes to gene loci, transcripts, exons and ncRNAs. BMC Bioinformatics.2010 Apr 29;11:221.
This data is the number of probes and the number of transcripts mapped to each gene for human exon chips.
data(Human_probes_transcripts)data(Human_probes_transcripts)
A 40174*2 matrix including the number of probes and the number of transcripts mapped to each of 40174 genes for human exon chips.
Risueno A, Fontanillo C, Dinger ME, De Las Rivas J. GATExplorer: genomic and transcriptomic explorer; mapping expression probes to gene loci, transcripts, exons and ncRNAs. BMC Bioinformatics.2010 Apr 29;11:221.
This data include the names of transcripts mapped to each gene for human exon chips.
data(Human_transcript_name)data(Human_transcript_name)
A 121741*1 matrix including 121741 transcript names mapped to genes for human exon chips.
Risueno A, Fontanillo C, Dinger ME, De Las Rivas J. GATExplorer: genomic and transcriptomic explorer; mapping expression probes to gene loci, transcripts, exons and ncRNAs. BMC Bioinformatics.2010 Apr 29;11:221.
This data include the coordinates of probes and the mapped transcripts for human exon chips.
data(Human_transcript_NO)data(Human_transcript_NO)
A 4598850*3 matrix including pos_x,pos_y and transcript_no. pos_x and pos_y are respectively X and Y coordinates of probes for human exon chips. Transcript_no is the mapped transcripts for each probe.
Risueno A, Fontanillo C, Dinger ME, De Las Rivas J. GATExplorer: genomic and transcriptomic explorer; mapping expression probes to gene loci, transcripts, exons and ncRNAs. BMC Bioinformatics.2010 Apr 29;11:221.
This data include the probes location for Mouse exon chips.
data(Mouse_Location)data(Mouse_Location)
A 1*1278936 matrix including the location for unique probes in Mouse_transcript_NO.
Risueno A, Fontanillo C, Dinger ME, De Las Rivas J. GATExplorer: genomic and transcriptomic explorer; mapping expression probes to gene loci, transcripts, exons and ncRNAs. BMC Bioinformatics.2010 Apr 29;11:221.
This data include the number of probes and the number of transcripts mapped to each gene for mouse exon chips.
data(Mouse_probes_transcripts)data(Mouse_probes_transcripts)
A 27719*2 matrix including the number of probes and the number of transcripts mapped to each of 27719 genes for mouse exon chips.
Risueno A, Fontanillo C, Dinger ME, De Las Rivas J. GATExplorer: genomic and transcriptomic explorer; mapping expression probes to gene loci, transcripts, exons and ncRNAs. BMC Bioinformatics.2010 Apr 29;11:221.
This data include the names of transcripts mapped to each gene for mouse exon chips
data(Mouse_transcript_name)data(Mouse_transcript_name)
A 75751*1 matrix including 75751 transcript names mapped to genes for mouse exon chips.
Risueno A, Fontanillo C, Dinger ME, De Las Rivas J. GATExplorer: genomic and transcriptomic explorer; mapping expression probes to gene loci, transcripts, exons and ncRNAs. BMC Bioinformatics.2010 Apr 29;11:221.
This data include the coordinates of probes and the mapped transcripts for mouse exon chips.
data(Mouse_transcript_NO)data(Mouse_transcript_NO)
A 2928848*3 matrix including pos_x,pos_y and transcript_no. pos_x and pos_y are respectively X and Y coordinates of probes for mouse exon chips. Transcript_no data is the mapped transcripts for each probe.
Risueno A, Fontanillo C, Dinger ME, De Las Rivas J. GATExplorer: genomic and transcriptomic explorer; mapping expression probes to gene loci, transcripts, exons and ncRNAs. BMC Bioinformatics.2010 Apr 29;11:221.
This data is taken from the estrogen package. It was created to be used in the vignette for the puma pacakge. It can be produced using the following code:
library(estrogen)
datadir <- file.path(find.package("estrogen"),"extdata")
estrogenFilenames <- c("low10-1.cel","low10-2.cel","high10-1.cel","high10-2.cel"
, "low48-1.cel","low48-2.cel","high48-1.cel","high48-2.cel")
setwd(datadir)
oligo.estrogen <-read.celfiles(
filenames=estrogenFilenames
)
pData(oligo.estrogen) <- data.frame(
"estrogen"=c("absent","absent","present","present"
,"absent","absent","present","present")
, "time.h"=c("10","10","10","10","48","48","48","48")
, row.names=rownames(pData(oligo.estrogen))
)
data(oligo.estrogen)data(oligo.estrogen)
An ExpressionFeatureSet object containing 8 HG\_U95Av2 arrays, in a 2 x 2 factorial design, with 2 replicates for each combination of factors. The factors are estrogen (absent of present) and time.h (10 or 48).
This data is taken from the estrogen package. It was created to be used in the vignette for the puma pacakge. It can be produced using the following code (note this could take a long time to run):
data(eset_estrogen_mmgmos) pumapca_estrogen <- pumaPCA(eset_estrogen_mmgmos)
data(pumapca_estrogen)data(pumapca_estrogen)
An pumaPCARes object containing principal components (created using pumaPCA) of 8 HG\_U95Av2 arrays, in a 2 x 2 factorial design, with 2 replicates for each combination of factors. The factors are estrogen (absent of present) and time.h (10 or 48).
data(pumapca_estrogen) plot(pumapca_estrogen,legend1pos="right",legend2pos="top")data(pumapca_estrogen) plot(pumapca_estrogen,legend1pos="right",legend2pos="top")
This data include the probes location for Rat exon chips.
data(Rat_Location)data(Rat_Location)
A 1*931210 matrix including the location for unique probes in Rat_transcript_NO.
Risueno A, Fontanillo C, Dinger ME, De Las Rivas J. GATExplorer: genomic and transcriptomic explorer; mapping expression probes to gene loci, transcripts, exons and ncRNAs. BMC Bioinformatics.2010 Apr 29;11:221.
This data is the number of probes and the number of transcripts mapped to each gene for rat exon chips.
data(Rat_probes_transcripts)data(Rat_probes_transcripts)
A 23585*2 matrix including the number of probes and the number of transcripts mapped to each of 23585 genes for rat exon chips.
Risueno A, Fontanillo C, Dinger ME, De Las Rivas J. GATExplorer: genomic and transcriptomic explorer; mapping expression probes to gene loci, transcripts, exons and ncRNAs. BMC Bioinformatics.2010 Apr 29;11:221.
This data is the names of transcripts mapped to each gene for rat exon chips
data(Rat_transcript_name)data(Rat_transcript_name)
A 334851*1 matrix including 334851 transcript names mapped to each gene for rat exon chips.
Risueno A, Fontanillo C, Dinger ME, De Las Rivas J. GATExplorer: genomic and transcriptomic explorer; mapping expression probes to gene loci, transcripts, exons and ncRNAs. BMC Bioinformatics.2010 Apr 29;11:221.
This data include the coordinates of probes and the mapped transcripts for rat exon chips.
data(Rat_transcript_NO)data(Rat_transcript_NO)
A 1491570*3 matrix including pos_x,pos_y and transcript_no. pos_x and pos_y are respectively X and Y coordinates of probes for rat exon chips. Transcript_no is the mapped transcripts for each probe.
Risueno A, Fontanillo C, Dinger ME, De Las Rivas J. GATExplorer: genomic and transcriptomic explorer; mapping expression probes to gene loci, transcripts, exons and ncRNAs. BMC Bioinformatics.2010 Apr 29;11:221.