WGLab/GenGen

calculate_gsea.pl P_PERM column not found

shraddhapai opened this issue · 2 comments

shraddhapai commented

Hi Kai,
Thank you for writing gengen; I use it in my projects for pathway analysis.

When the --pvalue_flag is set, calculate_gsea.pl seems to be searching for a column named "_P_PERM" rather than "P_PERM". I kept getting an error with a column named as the latter, and modifying line 306 to "P_PERM" fixed the issue.
Either the documentation needs to be fixed, or that line does, to clarify what header to expect.

Thanks and regards,
Shraddha

kaichop commented

The column name depends on how the permuted p-values are generated. I have updated the script to look for P_PERM instead.

shraddhapai commented