Dear Greg Thanks for your comment: Detailed description and a number of problems are described in my new BioC post with subject: Design question in LIMMA As for data preporcessing step I used ordinary: RG <- backgroundCorrect(RG,method="minimum") MA <-normalizeWithinArrays(RG, method="loess") MA <- normalizeBetweenArrays(MA, method="Aquantile") I didn't use weighting of the control spots (commercial Agilent 44K) and didn't used anything flaged by Feature Extraction. Maybe I have to? I visualize the data afterwards and they look not bad. I do understand that the data in topTable are in log2 scale, but the differences seem to me to be really small. The problem may come as well from the wrong design and contrasts created. I hope this makes clear procedures I used. Regards Nataliya Greg Finak wrote: > Hi, Nataliya. > > This is very much dependent on how you normalize your data. It's > possible to "over normalize" and wipe out most of the variability in > your data. If you're certain that this isn't the case, then, no, > Limma doesn't generate shrunken estimates of the expression ratios, > only t-statistics. The expression ratios presented by limma will > either be log2, or a data dependent scale if you've used VSN to > normalize. Feel free to post more information about your > normalization / preprocessing / experimental design, that would help > to identify potential reasons, otherwise we're just speculating. > > Cheers, > > > -------------------------------------------- > Greg Finak > PhD Candidate > McGill Center For Bioinformatics > > W: (514)398-7071 x09317 > emai: finak at mcb.mcgill.ca > -------------------------------------------- > > On 9-Nov-05, at 7:13 PM, Nataliya Yeremenko wrote: > >> Hello everybody >> >> After successful importing the data to the LIMMA, >> I followed all steps and finally obtained "topTable". >> (the data were 44K Agilent) >> I'm surprised that my data set doesn't have anything with M-values more >> than 1.5. >> I well understand that it depends on the experiment, >> but is there some condensation of the Ratio during normalization and >> other procedures? >> >> regards >> >> -- >> Dr. Nataliya Yeremenko >> >> Universiteit van Amsterdam >> Faculty of Science >> IBED/AMB (Aquatische Microbiologie) >> Nieuwe Achtergracht 127 >> NL-1018WS Amsterdam >> the Netherlands >> >> tel. + 31 20 5257089 >> fax + 31 20 5257064 >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor > > > > -- Dr. Nataliya Yeremenko Universiteit van Amsterdam Faculty of Science IBED/AMB (Aquatische Microbiologie) Nieuwe Achtergracht 127 NL-1018WS Amsterdam the Netherlands tel. + 31 20 5257089 fax + 31 20 5257064