The question on having "more appropriate background distributions" has more to do with having sufficient sample size for the first step in which GSVA evaluates whether a gene is highly or lowly expressed in a sample. But I understand your question is rather about the input number of genes. As d ...
regarding ssGSEA, I implemented the method in the GSVA package but I did not developed it; see the original publication by Barbie et al. (2009) for the methodological details. My understanding is that it was designed for microarray data (see documentation of its official implementation in GeneP ...
we chose this fixed setting because from our experience it worked well in practice.
you have a typo in your code, the '==' operator is for comparison, not for assignment. please replace
method == "ssgsea"
method = "ssgsea"
and it will work.
... Dear Fazulur,
1. No, you can not use RPKM values as input to the tweeDEseq package. This package implements a statistical model based on Poisson-Tweedie distributions for count values and RPKM values are not count values.
2. No, for the same reason I give on your first question.
As a side note, w ...
I've just tried it out with the current release version of R 3.4.2 and the GSEABase package (1.40.1) and it works fine. You need to update to the current R release version 3.4.2 and current release of Bioconductor; see http://bioconductor.org/install.
MSigDB <- getBroadS ...