Dear Roger, I think there is no a default value for the FDR in the toptable funtion. You will get a p-values corrected by the method you choose(fdr, bh).
Briefly the shorted list of p-values will give you the FDR. It is up to you choose what is the estimated number of false positives you want to have. HTH Manuel --- "Vallejo, Roger" <[EMAIL PROTECTED]> escribió: > Dear R-Help, > > > > I am using the function "topTable" from the LIMMA > package. To estimate > adjusted P-values there are several options > (adjust="fdr" , adjust="BH") > as shown below: > > > > topTable(fit, number = 10, adjust = "BH", fit$Name) > > > > > I guess any of these options (fdr, BH, etc.) is > using a default of > FDR=0.05 which is quite conservative (i.e., very > likely none of the > tested genes will be ranked as differentially > expressed at 5% FDR). I > would argue that for an exploratory study it would > be okay to use a 0.05 > < FDR <0.20. So, I was wondering if we can change > that default of > FDR=0.0.5 with a less stringent FDR value (0.10, > 0.20, etc.) in the > "topTable" function. How do I change it? > > > > Thanks a lot for the help on the use of "topTable" > function from the > LIMMA package. > > > > Roger > > > > > > Roger L. Vallejo, Ph.D. > > Computational Biologist & Geneticist > > U.S. Department of Agriculture, ARS > > National Center for Cool & Cold Water Aquaculture > > 11861 Leetown Road > > Kearneysville, WV 25430 > > Voice: (304) 724-8340 Ext. 2141 > > Email: [EMAIL PROTECTED] > <mailto:[EMAIL PROTECTED]> > > > > > [[alternative HTML version deleted]] > > ______________________________________________ > [email protected] mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide > http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, > reproducible code. > ______________________________________________ [email protected] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
