GSVA analysis to comparison
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3 months ago
psundar2 • 0

My initial data is raw RNA Seq Count data. I then used DESeq2 to normalize the data which I then put through GSVA. Now that I have the enrichment scores from GSVA, here is my problem. So my GSVA scores has the pathways as the row names and the sample as the column name. Now I want to compare samples within each pathway such that I can output the logFC and p value for each comparison. How would I go about doing that and what would my next step be after GSVA?

GSVA • 280 views
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Entering edit mode
3 months ago
jv ▴ 400

The GSVA documentation has a step-by-step example of using limma to assess differential pathway enrichment. See 6.2 Differential expression at pathway level

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