Hi I was just browsing through my collection of papers and came across this one: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&d op t=Abstract&list_uids=12584122 Here Benjamini has released an R script that analyses microarray data and controls for the FDR. I notice also that limma controls for the FDR, and wondered if/how the two analysis methods compared, both in theory/philosophy and in practice. Any comments would be appreciated Mick