GSVA Setup

Question

[michaelhojungyoon]

New to using gsva. From my understanding, I believe you require an expression matrix (gene x samples) and sets of genes stored as a list to run gsva().

However, if my downstream analysis is only interested in samples of a certain timepoint (e.g. I'm interested in control vs disease for samples at timepoint 4h), would I filter out the expression matrix to include only these samples while creating the gsva() object? Are the other samples seen as confounders?

Answer 1

[yura.grabovska]

By definition gsva() is single-sample enrichment method (more info here) which means that other samples in the set are not part of the calculation.