Ovarian Cancer

Mike Birrer   Curtis Huttenhower   Giovanni Parmigiani   Levi Waldron

Please report any issues using the issue tracking system, and obtain official releases from the Bioconductor curatedOvarianData site.

The curatedOvarianData R package provides gene expression data for ovarian cancer with accurately curated clinical annotations. The datasets are documented, probesets are mapped to standard HGNC gene symbols, and made available as Bioconductor ExpressionSet objects. Please cite this package as:

Benjamin Frederick Ganzfried, Markus Riester, Benjamin Haibe-Kains, Thomas Risch, Svitlana Tyekucheva, Ina Jazic, Xin Victoria Wang, Mahnaz Ahmadifar, Michael J. Birrer, Giovanni Parmigiani, Curtis Huttenhower, and Levi Waldron. curatedOvarianData: clinically annotated data for the ovarian cancer transcriptome. Database 2013: bat013 doi:10.1093/database/bat013 published online April 2, 2013. (Bibtex)

(Authors BFG and MR contributed equally).

Three versions of the package are available:

  • curatedOvarianData: selects the probeset with maximum mean across all datasets of the same platform to represent each gene (collapseRows function). A table of the probesets used can be found in the featureData slot of each ExpressionSet.
  • NormalizerVcuratedOvarianData: discards probesets with expression patterns more similar to background than to other probesets for the same gene, then averages any remaining probesets, if any are remaining (http://huttenhower.sph.harvard.edu/sleipnir/Normalizer.html, with option -T medmult).
  • FULLVcuratedOvarianData: does not collapse redundant probesets at all, and just provides original probesets along with a map in the featureData ExpressionSet slot which may be used to do any mapping.

The official release version is available from the Bioconductor curatedOvarianData site. This page provides archived, development, and alternative versions.

The pipeline used for creating this package is a publicly available open-source project, with version control and a mailing list.

Here are the changelog file, vignette, and reference manual.

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