I want to do a pathway enrichment analysis (GSEA method) by using the gene ranking file generated by the Mageck test command and a GMT file. This type of analysis can be performed by using the Mageck pathway command:
mageck pathway --gene-ranking rank.txt --gmt-file file.gmt -n name
Firstly, the output generated was incomplete because the pathway id column of the GMT file contained white spaces and I replaced them by "_". But now I observed that in the output the description words of the second column are counted as genes. How can I solve this?