Dear Bioconductors, I came across the following problem after I switched my work to another computer, install the R 2.8.0. The same code works fine in my old computer with R 2.7.2. I would like to ask for your help. Problem: If I type in: TB <- topTable(fit3, coef=1, p=0.05, lfc=2, n=1000, adjust="BH") I will get an error Error in M[sig, ] : incorrect number of dimensions However, if I change the command to TB <- topTable(fit3, coef=1, p=1, lfc=0, n=1000, adjust="BH") It works fine. So, it seems like the error comes up whenever I need to cutoff some of the probes. Here is my sessionInfo: R version 2.8.0 (2008-10-20) i386-pc-mingw32 locale: LC_COLLATE=English_United States.1252;LC_CTYPE=English_United States.1252;LC_MONETARY=English_United States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252 attached base packages: [1] tools stats graphics grDevices utils datasets methods [8] base other attached packages: [1] statmod_1.3.6 vsn_3.8.0 affy_1.20.0 Biobase_2.2.0 [5] lattice_0.17-15 limma_2.16.2 loaded via a namespace (and not attached): [1] affyio_1.10.1 grid_2.8.0 preprocessCore_1.4.0 Thank you very much! Zhuoxun Chen [[alternative HTML version deleted]]