Due to some issues with the way DEXseq calculates the log2foldchanges I decided to re-run an analysis with the issue fixed. Since it is not yet in the development branch, an install from svn was needed – my first!
Firstly the source code was downloaded with:
svn co --username readonly --password readonly https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_0/madman/Rpacks/DEXSeq DEXSeq
This followed a build to generated a package:
R CMD build --no-build-vignettes DEXSeq
I had issues with the build process, which failed during the vignette build. As I don’t care about it, using
--no-build-vignettes bypassed the problem. Then it was a simply matter of starting R and installing the package: