Which plan is more reasonable, gsea on total dataset , on subset of total dataset with DEG or preRanked gsea?
Hi Dears I have an expressionSet including case and control samples, I did DEG analysis with limma, now I want to do gsea analysis for 2 phenotype , but I am hesitate about choosing above mentioned approachs and which one is more reasonable
- gsea on total dataset including case and control
- gsea on subset of total dataset with DEG between case and control that come from limma toptable output
- preRanked gsea (including a ranked gene list )
Thanks in advance
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Shamim Sarhadi
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