I want to use `camera` function in limma. I downloaded xml file from MSigDB and loaded it but I am wondering how can I make it to a compatible list for camera function as it has been mentioned in here that GEneCollection need to be converted to a list.
what I have done is
gsc <- getBroadSets("P:/repos/R/msigdb_v6.1.xml") camera(eset, design = design, index = gsc[grepl("REACTOME", names(gsc))]) Error in Stat[iset] : invalid subscript type 'S4'
This code works when I load the file from http://bioinf.wehi.edu.au
download.file("http://bioinf.wehi.edu.au/software/MSigDB/human_c2_v5p2.rdata", "human_c2_v5p2.rdata", mode = "wb") load("human_c2_v5p2.rdata") camera(eset, design = design, index = Hs.c2[grepl("REACTOME", names(Hs.c2))])