u/EmotionalRemote6217

SO! my RDA and PCA are both not significant. However, i am pushing through this given it’s a master’s thesis and I will be transparent about this.

When I do DEG with padj, I don’t get anything significant. But I can get some genes with pvalue<0.01 and 0.05.

This is why I decided to do GSEA instead of ORA. However, I did GSEA with only my genes after pre-filtering (10 counts in smallest group size) but didn’t include a specific gene set… is that ok?

I am blasting my organism against a decently annotated relative. Should I create my own gene set from its entire genome? One that is related to my research question?

I hope i’m clear!

TLDR: do i need a gene set or can i do GSEA with pre-filtered RNA counts only