I have some problems with run_edgeR or run_DESeq2 functions from systempipeR package. I 've done all required steps described in vignette and when I've tried to do run_edgeR by command:
edgeDF <- run_edgeR(countDF = countDF, targets=targets, cmp=cmp[], independent=FALSE, mdsplot="")
I've had an error like this:
Error in `[.data.frame`(countDF, , names(samples)) :
undefined columns selected
Maybe, I've created targets.txt file in wrong way or somthing else. So, I have no problems using my set of BAM files in DESeq2 package and edgeR package, but I need to use run_edgeR (or run_DESeq2) from systempipeR because I want to use GO term enrichment analysis of DEGs from this package.
Thank you in advance,