Let's suppose I have gene expression table consisting of 100 samples.
The samples can be grouped as A, B, C, and D. I want to compare the pathway scores between A, B, and D.
Here's my two options : (i) run GSVA to whole 100 samples, and compare the GSVA scores between A, B, and D (ii) extract the A, B, D samples first, and then run the GSVA to that filtered table, followed by comparison of GSVA scores
Would these two give any differences? In addition, since I'm going to run statistical tests (such as ANOVA) when comparing the GSVA scores between A, B, and D, might those two options even affect statistical significance?
As I understand, unlike ssGSEA which may not care about other samples when calculating, GSVA accounts for the other samples too, so the two methods may have difference.
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