To: tom pope who wrote (198 ) 2/3/2004 4:20:00 PM From: tuck Read Replies (3) | Respond to [reproducibility of SELDI experiments]clinicalproteomics.steem.com . In general, the results were not reproducible across experiments. Baseline correction prevents reproduction of the results for two of the experiments. In one experiment there is evidence of a major shift in protocol mid-experiment which could bias the results. In another, structure in the noise regions of the spectra allows us to distinguish normal from cancer, suggesting that the normals and cancers were processed differently. Sets of features found to discriminate well in one experiment do not generalize to other experiments. Finally, the mass calibration in all three experiments appears suspect. Taken together, these and other concerns suggest that much of the structure uncovered in these experiments could be due to artifacts of sample processing, not to the underlying biology of cancer. We provide some guidelines for design and analysis in experiments like these to better ensure reproducible, biologically meaningfully results. AVAILABILITY: The MATLAB and Perl code used in our analyses is available at bioinformatics.mdanderson.org.<<
