Entering edit mode
Hi all,
I hope to get some clarification regarding the sorting of log2FC or FC for GSEA.
In decreasing order, the positive log2FC would make sense as larger absolute values will be at the top of the list, but negative FC values with larger absolute values (i.e., smaller negative FC) will be deprioritised and placed at the bottom of the ranked gene list.
Does this mean I should order the negative FC in an increasing order while ordering the positive FC in a decreasing order?
Thank you for your help!
Thank you ATpoint for your response!
In the result of GSEA, like you indicated, there will be gene sets that have positive NES and gene sets that have negative NES values
(scoreType = "std"). Assuming the ranked (by log2FC) list of genes that was used for this GSEA was derived from DESeq comparing Subset1 vs Subset2 (Subset2=reference). This list again has both negative and positive log2FC genes.Might I ask if it is accurate to interpret/infer that among p.adjust <0.05 gene sets from GSEA, NES>0 gene sets were significantly enriched in Subset1, and NES<0 gene sets were significantly enriched in Subset2?
Or, would I need to do a separate DESeq comparing Subset2 vs Subset1 (setting Subset1 as reference) to get the significantly enriched gene sets for Subset2?
I asked because the GSEA result (from input list of comparing Subset1 vs Subset2), the significant gene sets were all NES>0.
Thank you again for your help!