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.
