Dear all, I recently encountered a problem subsetting limma TestResults on a new Bioconductor install. If I do > results<-decideTests(fit3,adjust="holm") > results[results<0] to extract differentially expressed genes from a MOE4302 fit I will get a matrix with results and Affy ID > results[results<0] 1427262_at 1427263_at 1436717_x_at ... -1 -1 -1 ... in R 2.1.1, limma 2.0.8 on OSX 10.4.6/PPC, but > results[results<0] [1] -1 -1 -1 -1 -1 -1 -1 -1 -1 ... in R 2.3.0, limma 2.7.3 on OSX 10.4.6/PPC, that is, the results without Affy ID . Same if I use subset(results, results<0). Since I really would like to retain the Affy IDs in the subset for further annotation - am I missing something here, and is there a way to make this work again ? Thanks, Michael