Hi all,
I'm comparing RNA-seq data that come from mammalian cells exposed to two different strains of a fungus. I'm interested in separately analyzing the genes differentially expressed in response to the strains individually, but also in the genes that are differentially expressed in response to both strains.
The problem I'm running into is that the DE genes that are shared between strains have different logFC or FDR values for each strain, so is there a way for me to possibly generate a .rnk file to do GSEA???
1 answer
Do you have control samples (i.e. non exposed cells)? It sounds like you are performing two separate DE analyses:
Strain A vs. Control
Strain B vs. Control
and now you would like to combine them in some way and perform GSEA? You could consider performing a single DE analysis across strains:
Strain A + Strain B vs. Control
Then you would get a single logFC / FDR per genes. I say 'could consider' because it will depend on the study design and how data were generated.
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