I am trying to retrieve up/down gene expression scores using the LINCS L1000 landmark gene set. I have the gctx and csv files provided from the L1000FWD page:

http://amp.pharm.mssm.edu/l1000fwd/download_page

I am able to retrieve the list of significantly differentially expressed genes from the CD_signature_metadata.csv file, however, I would like to rank these genes by their expression score. I believe the data could be inside the CD_signatures_LM_42809x978.gctx file although I am not certain by any stretch of the imagination. There is an R package, cmapR with a function parse.gctx. However, I am hoping someone with a lot more experience in CMAP/LINCSL1000 could provide some helpful suggestions.

Thanks