Hello everyone, I am starting to analyze a dataset from Affymetrix's E.coli genome 2.0 arrays, and I'm running into several weird things. This is the first time I've handled prokaryotic data, so I don't know if that's the reason it looks so different from most eukaryotic data I've seen. I would really appreciate it if anyone with E. coli experience would be willing to have an extended discussion off-line. Additionally, here are two issues on which I'd love some comments: 1. The histograms of the raw pm & mm values are bimodal (see ftp://keck1.biotec.uiuc.edu/pub/Drnevich/Ecoli/ for output from signalDist). The most extreme array (# 9) had some problems with the labeling and hybridization, but it does appear to be at the end of a continuum. Looking through the Bioconductor archives, others have commented that bimodality may not be a problem in itself, but I wonder if anyone else has seen data this extreme or would be suspicious? The five arrays that different than the rest are from an different experimental treatment, which leads me to believe that this might be real data... 2. Applying bg.adjust.gcrma to the data results in almost zero expression for all pm probes! (see link above). I doubt that all the expression is due to non-specific binding and/or probe affinity. Is it likely that the different labeling of prokaryotic samples (N-terminus) would render gcrma background correction unusable? Thanks so much for any comments! Jenny Jenny Drnevich, Ph.D. Functional Genomics Bioinformatics Specialist W.M. Keck Center for Comparative and Functional Genomics Roy J. Carver Biotechnology Center University of Illinois, Urbana-Champaign 330 ERML 1201 W. Gregory Dr. Urbana, IL 61801 USA ph: 217-244-7355 fax: 217-265-5066 e-mail: drnevich at uiuc.edu