GSVA analysis to comparison

Question

[psundar2]

My initial data is raw RNA Seq Count data. I then used DESeq2 to normalize the data which I then put through GSVA. Now that I have the enrichment scores from GSVA, here is my problem. So my GSVA scores has the pathways as the row names and the sample as the column name. Now I want to compare samples within each pathway such that I can output the logFC and p value for each comparison. How would I go about doing that and what would my next step be after GSVA?

Answer 1

[jv]

The GSVA documentation has a step-by-step example of using limma to assess differential pathway enrichment. See 6.2 Differential expression at pathway level