I want to ask a question whether it is possible to compare two or more GSVA outputs (of same gene sets), when it is not possible to merge the data (i.e. too large gene expression data matrix for GSVA to run) and run GSVA at once.
It looks like when there are too many samples, GSVA takes too much time to run, or even have no progress even after long time of waiting. I'm curious if it is possible to split the samples into two or more groups, run GSVA separately to each groups, and compare the GSVA values with each other.
If it is not possible or right to do so, is there any way to do instead?
Thank you very much.