Dear List, I'm trying to confirm the default fdr rate (for the BH method) in limma & also in affylmGUI. I failed to extract this information from list archives or the manual. Does anyone know what it defaults to when not specified? And out of curiosity, where/how is this information obtained/confirmed? thanks in advance, Karl -- *new phone numbers* Karl Brand <k.brand at="" erasmusmc.nl=""> Department of Genetics Erasmus MC Dr Molewaterplein 50 3015 GE Rotterdam lab +31 (0)10 704 3409 fax +31 (0)10 704 4743 mob +31 (0)642 777 268

Hi Karl, k. brand wrote: > Dear List, > > I'm trying to confirm the default fdr rate (for the BH method) in limma > & also in affylmGUI. I failed to extract this information from list > archives or the manual. That is a pretty broad question. What particular function are you talking about? I don't know that you can assume all functions in both packages that adjust for multiplicity use the same correction. However, this info can be had in (at least) two ways. Say you want to know about topTable(). ?topTable gives me Usage: topTable(fit,coef=NULL,number=10,genelist=fit$genes,adjust.method="BH" ,sort.by="B",resort.by=NULL,p.value=1,lfc=0) Further, args() gives me this: > args(topTable) function (fit, coef = NULL, number = 10, genelist = fit$genes, adjust.method = "BH", sort.by = "B", resort.by = NULL, p.value = 1, lfc = 0) You could also just type topTable at an R prompt and scroll back to the top of the function to see what the defaults are. Best, Jim > > Does anyone know what it defaults to when not specified? And out of > curiosity, where/how is this information obtained/confirmed? > > thanks in advance, > > Karl > > -- James W. MacDonald, M.S. Biostatistician Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109 734-647-5623