DE gene analysis

Question

[priyas772]

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!

Answer 1

[mforde84]

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.

[priyas772]

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

[mforde84]

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