Mageck pathway command output error
Entering edit mode
18 months ago

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?

gsea mageck pathway • 468 views

Login before adding your answer.

Traffic: 1396 users visited in the last hour
Help About
Access RSS

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6