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DE gene analysis

I performed differential gene analysis on two GEO datasets using NetworkAnalyst , i found set of up- and down- regulated genes using Fisher's method. Since I am new to the area of analysis , i wanted to know how to further proceed with the analysis to find a biomarker Thank You!

de genes
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updated by mforde84 mforde84 • written by priyas772 • priyas772

1 answer

Gene set enrichment analysis is a good next step. You can do a contrast based analysis with something like EGSEA, or you can do per sample enrichment scores with GSVA.

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written by mforde84 mforde84

Hii! Is there any codes available for doing the enrichment analysis using EGSEA in R?

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written by priyas772 • priyas772

Yes. The package has plenty of documentation and working code samples.

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written by mforde84 mforde84

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