Hey community members,
I have a question using GSVA for Nanostring data (789 targeted genes per sample). I know previously there was discussion here about using GSVA for Nanostring, and the big thing is to decide appropriate argument for kcdf (https://support.bioconductor.org/p/111096/).
My question is: 1) In literatures, I have seen people using both GSVA and ssGSEA for Nanostring and I am not sure why. I am wondering if there is a preferred method for targeted gene panel in general. 2) I used DESeq2 in my pipeline. Interestingly I got very different GSVA results when using normalized counts as input (with kcdf = "Poisson") versus when using rlog as inputs (with kcdf = "Gaussian") . I am wondering how to explain the discrepancy and which method is better.
Many thanks for the kind help.