I want to perform GSEA analysis on a list of genes. Out of the following two options, which one should I use and why?
List of all genes with their log-fold-change values.
filtered list of genes with their log-fold-change values. Here, the filter could be p-value, FDR or filtering based on absolute log-fold-change of 0.5
To me, option 1 might give some false positives. And, option 2 might be biased as I am already filtering out the genes with the arbitrary cut-off.