Just wanted to describe a bug I'm getting for the GSVA package.
This little code bit should calculate a little TLR4 signaling pathway on the dataset.
rm(list=ls()) library(GSVA) library(leukemiasEset) data(leukemiasEset) dat <- exprs(leukemiasEset) TLR4 = 'ENSG00000136869' MYD88 = 'ENSG00000172936' plot(x=dat[TLR4,],y=dat[MYD88,]) gset = list(LPS=c('ENSG00000136869','ENSG00000172936')) pathway <- gsva(dat, gset)$es.obs plot(x=dat[TLR4,],y=pathway['LPS',])
But this bit of code produces opposite GSVA scores when computed on mac and windows.
Mac was done on R 3.4.2 with Bioconductor 3.6, and Windows was R 3.4.1 with Bioconductor 3.6.
You can see the Windows correlation looks right, but Mac is the opposite.
And on Mac OS the same bit of code is this:
I'm not sure how to page the package owner on this forums or if there is a more appropriate place for this post. But it should be of general interest to anyone who sees that their GSVA results on Mac are opposite of what they expect.. positive and negative switch.
Edit: I've sent an email to the package maintainer to let them know of the problem.
The Bioconductor version (3.6) for R 3.4.2 is not released yet. You seem to be aware that it is on development but the package might change before the release to be consistent between OS.