I have several tables of results from different DESeq2 runs. The next step would be to do GO enrichment or GSEA enrichment analysis.
For that I would like to create a ranked list of genes for GSEAPreRanked. But I'm not sure which value to take for the ranking. Do I use the log2FC values or the p-values, or even the adjusted p-values.
I have searched in different foren and the opinions varied.
When I use this command
sign(resultsObject$log2FoldChange) * -log10(resultsObject$padj) I get
Inf, if the
FOr the GO enrichment I can use the
goseq package, for the gsea I wanted to use
fgsea, which does need a ranked gene list.
Is it better to rank the list by significance (adj. p-values) or by expression intensity ( fold-change)?
I would appreciate your opinions and/or reccomendations