Just a suggestion: The FDR adjusted "p-values" are called "q-values" in much of the literature. I suggest that limma follow suit, and also add a line to the documentation (it might already be there and I missed it) "If the number of significant results at level alpha is less than alpha*(number of genes), then the q-value will be 1.0." It seems like I have to explain this to just about every investigator who runs into this. Naomi S. Altman 814-865-3791 (voice) Associate Professor Bioinformatics Consulting Center Dept. of Statistics 814-863-7114 (fax) Penn State University 814-865-1348 (Statistics) University Park, PA 16802-2111