search for: ids2

Hi R friends! I am stuck with a stupid question: I can circumvent it but I would like to understand why it is wrong. It would be nice if you could give me a hint... I have an 2D array d and do the following: ids <- which(d[,1]>0) then I have a vector gk with same column size as d and do: ids2 <- which(gk[ids]==1) but I can't interprete the result I get in ids2. I get the expected result when I use: which(gk==1 & d[,1]>0) Why is the first version wrong? The reason why I try to use the ids vectors is that I want to avoid recomputation. Thanks for your help! Werner

Hi, I'm using GAGE/pathview to analyze my RNA-seq and phospho-protein data. The following error occurs after this command line below: >pv.out.list <- sapply(path.ids2[1:3], function(pid) pathview( gene.data = cnts.d, pathway.id = pid, gene.idtype="SYMBOL",kegg.native = F, same.layer = T, species = "hsa", kegg.dir = "test", out.suffix = "up")) Start tag expected, '<' not found Warning: Parsing test/hsa04510...