Run Batch Effects and Ovarian Cancer

This web page contains supporting material for the manuscript Run batch effects potentially compromise the usefulness of genomic signatures for ovarian cancer, by Keith A. Baggerly, Shannon Neeley, and Kevin R. Coombes.

Here is a list of the available material. The main manuscript and supplementary reports are in PDF format. The source code, intermediate results, and public data sources are in zip files, starting from a common directory.

• Source Code (50 KB)
• Supplementary reports:
  • Supplementary Report ovca01 (3074 KB)
  • Supplementary Report ovca02 (110 KB)
  • Supplementary Report ovca03 (99 KB)
  • Supplementary Report ovca04 (125 KB)
  • Supplementary Report ovca05 (2435 KB)
  • Supplementary Report ovca06 (906 KB)
  • Supplementary Report ovca07 (797 KB)
• Intermediate results:
  • Figures (1906 KB)
  • LaTeX (1553 KB)
  • RDataObjects (194405 KB)
  • Tangled (15 KB)
• Public data sources:
  • BerchuckClinCancRes05 (223641 KB)
  • BildNature06 (503423 KB)
  • DressmanJCO07 (3 KB)
  • GEO (3219 KB)

Our analysis source code relies on a number of software programs and auxiliary packages; we provide scripts, not stand-alone executables. Detailed descriptions of the packages (with version numbers) are listed in the methods section of the main manuscript. The pieces of software required to execute the source code can be obtained from the following locations:

• The main program and several package libraries from the R environment for statistical programming.
• Several package libraries from BioConductor.
• Several package libraries from OOMPA.
• A working version of LaTeX, the text formatting system based on the work of Donald Knuth.
• The commercial softare program MATLAB

This page was produced on: Wed Dec 5 14:54:19 2007 GMT. Our intention is to avoid changing the files posted here, allowing the web site to serve as permanent documentation of our analysis. Any changes will be posted on a separate page designed for addenda, errata, corrigenda and other related latinisms.