The gene annotation information is usually a list component called 'genes' within the output object from lmFit, and eBayes. This gets used in the construction of the table of the top-ranked genes using topTable. Have a look at fit2$genes (for your object fit2). Your R expression has just provided a logical vector of corrected p-values for genes <0.05 based on the B&H's stepup FDR control, try: fit2$genes[selected.dif,] Marcus >>> Marcelo Luiz de Laia <mlaia@fcav.unesp.br> 17/02/2005 12:08:53 PM >>> Hi, I have been analyse a time course experiment with limma and I get the end of section 16 in userguide very well. But, I don't know how do I do to get the names of genes differentially expressed! For example, I do: selected.dif <- p.adjust(fit2$F.p.value, method="fdr") < 0.05 In object *selected.dif* I see that there are a lot of TRUE, but I don't know is their names! Any help is very appreciated. Marcelo -- No virus found in this outgoing message. Checked by AVG Anti-Virus. _______________________________________________ Bioconductor mailing list Bioconductor@stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/bioconductor ______________________________________________________ The contents of this e-mail are privileged and/or confidenti...{{dropped}}