Irreproducibility of NCI60 Predictors of Chemotherapy

This web page contains supporting material for the manuscript Genomic signatures based on the NCI60 cell lines do not predict patient response to chemotherapy, by Kevin R. Coombes, Jing Wang, and Keith A. Baggerly.

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.

• Main Supplement (SR0) (223 KB)
• Source Code (449 KB)
• Supplementary reports:
  • Supplementary Report SR1 (75 KB)
  • Supplementary Report SR2 (92 KB)
  • Supplementary Report SR3 (197 KB)
  • Supplementary Report SR4 (87 KB)
  • Supplementary Report SR5 (158 KB)
  • Supplementary Report SR6 (1496 KB)
  • Supplementary Report SR7 (166 KB)
  • Supplementary Report SR8 (116 KB)
  • Supplementary Report SR9 (418 KB)
• Intermediate results:
  • Figures (544 KB)
  • LaTeX (1192 KB)
  • MatlabFIles (27039 KB)
  • RDataObjects (79624 KB)
  • Results (20 KB)
  • Tangled (21 KB)
• Public data sources:
  • Chang (5508 KB)
  • DukeWebSite (14559 KB)
  • NatureMedicine (15 KB)
  • NCI60Processed (10698 KB)
  • NCI60Raw (71541 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: Fri Aug 24 18:10:47 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.