NEWS

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curatedOvarianData 1.5.2

• Fixed bugs in createEsets.R

curatedOvarianData 1.3.2

• Updated all gene maps

curatedOvarianData 1.3.1

• Added missing grade to GSE26913
• Improved order of gene filtering in createEsetList.R

curatedOvarianData 1.3.0

• Added datasets: GSE26193, GSE49997, GSE44104, GSE51088
• Curated debulking status for Mok (GSE18520)
• Added sample_type classifications
• Refined platform_accession and metadata column names
• Upgraded to Ensembl release 76 for gene maps

curatedOvarianData 1.2.2

• Added "Non-unique gene symbols" section to vignette
• Updated createEsetList.R and patient selection config

curatedOvarianData 1.2.1

• Fixed curation of TCGA sample type "11"

curatedOvarianData 1.2.0

• Added RNA-seq TCGA data
• Updated gene maps

curatedOvarianData 1.1.1

• Added options remove.retracted and remove.subsets to createEsets.R

curatedOvarianData 1.1.0

• Added p-values to figure captions
• Renamed package variants in inst/extdata/*
• Updated metadata for GSE18520
• Added GSE8842 (Agilent array)
• Added DATABASE publication citation

curatedOvarianData 1.0.1

• Curated grade for GSE17260

curatedOvarianData 1.0.0

• Automated per-dataset documentation
• Expanded vignette
• Added missing grade/summarygrade fields
• Enriched ExpressionSets with metadata
• Fixed TCGA experiment name typo
• Fixed featureData in FULLV version

curatedOvarianData 0.99.21

• Improved merging logic for technical replicate metadata

curatedOvarianData 0.99.20

• Added stromal/tumor/normal cell percentages
• Added uncurated_author_metadata
• Removed obsolete metadata fields
• Renamed metadata fields
• Defined TCGA optimal debulking as <10mm

curatedOvarianData 0.99.10

• Added TCGA-mirna-8x15kv2 and GSE30161

curatedOvarianData 0.99.2

• Added tumorstage and summarystage to GSE26712

curatedOvarianData 0.99.1

• Fixed expO short title
• Updated staging system in template
• Curated stage/grade fields in multiple datasets
• Added tumorstage to GSE2109
• Removed curation files for uncurated datasets
• Fixed stage data in GSE6008
• Updated BLAST reference genome to GRCh37.68
• Updated BioMart gene maps
• Addressed missing publication metadata
• Made test_counts.R work
• Handled metadata disagreement in technical replicates
• Added batch variable to GSE17290060

curatedOvarianData 0.5.0

• Disallowed "unknown" in templates; use NA instead
• Added syntax-checking unit test

curatedOvarianData 0.4.2

• Actually included ages for GSE26712

curatedOvarianData 0.4.1

• Added ages to GSE26712
• Used getPlatformsBiomaRt for GSE6822

curatedOvarianData 0.4.0

• Added GSE30009 (Taqman qPCR dataset)

curatedOvarianData 0.3.0

• Added GSE32062.GPL6480 and GSE32063
• GSE13876: removed redundant recurrence status
• Resolved missing ExperimentData for GSE2109 and GSE6822
• Added subtype information to multiple datasets
• Converted dataset check test to R CMD check unit test

curatedOvarianData 0.2.4

• TCGA: replaced missing batch variable
• GSE9891: corrected survival data for three patients

curatedOvarianData 0.2.3

• Renamed batch variables for consistency
• Consistently label missing debulking status as NA
• Replaced missing probesets in FULL version
• Added unit test for sample counts (not yet functional)

curatedOvarianData 0.2.2

• Replace GSE17260, which was missing in 0.2.1

curatedOvarianData 0.2.1

• In the TCGA dataset, about 40 censored patients had days_to_death and days_to_recurrence labelled as NA instead of follow-up time.
• TCGA released updated clinical information for six patients
• Minor changes to GSE18520 based on a review, including updates to debulking status, stage, and grade.

curatedOvarianData 0.2.0

• Added E-MTAB-386 (FFPE samples with survival data)
• Put MaxMean probe mappings in eset@featureData
• Put official Bioconductor platform names in eset@annotation