Hi,

I am eager to apply GSVA but have a following question:

I installed the package from Bioconductor (GSVA_1.46.0). When I run GSVA, the options mx.diff and abs.ranking make difference only for when the method is "gsva" and not for "ssgsea". From the documentation, it is not clear if this option should be applicable to both the analysis methods or is it some kind of bug.

Please let me know.

Hi,

I'm sorry about the confusion, the mx.diff and abs.ranking only apply when method="gsva". The documentation assumes to some extent that the user is familiar with the method that he/she wants to apply, and therefore, familiar with the parameters that wants to tune. We will be working during the next development cycle to avoid this confusion and improve the documentation. The only parameters that apply when method="ssgsea" are tau and ssgsea.norm.

cheers,

robert.