Regarding GSEA analysis

[Anirban Roy]

Hi, I am new to GSEA analysis. I have RNA seq data with fold change, log2-fold change, p values and FDR.

1. For GSEA analysis, should I use fold change or log2-fold change values?

2. Should I use all the genes that are differentially expressed in the gene list?

or should I use only the ones with a set p value? 

Thank you,

Anirban 

[Yuxing Liao]

Hi Anirban,

1. I would recommend log2 transformed values, especially if you have a few ones with very large fold changes.

2. Just use all genes. No significant ones are used like background.

Yuxing

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