Question About The Music Pathscan Fdr Value

Question

[xiaoqiaoliu]

I have a basic question for the FDR output of pathscan integrated in music.

According to my shallow understanding for multiple test correction, the corrected q-values will retain the order of p-values regardless of the correcting methods. Am I right? Yet, for the output of pathscan, I found that is not the case such as the following two items. I have ignored some columns such as Name and etc.

     Pathway    p-value         FDR
     05213      0.0036179       0.03765905
     04270      0.0041739       0.0092798359223301

And below is my command

     genome music path-scan --bam-list bam_list  --gene-covg-dir ../bmr_calc/gene_covgs/ --maf-file merge_all.maf --output-file pathscan_result --pathway-file music_pathscan_pathway_file_go_bp --bmr 4.0422059127903e-06

Is that the expected behavior for the FDR correction for pathscan? And if that is the case, what is the correcting method used by pathscan?

Look forward to your response.

[Cyriac Kandoth]

You are correct that FDR values should be in the same order as the p-values. The PathScan author is looking into this, and will provide an answer <del>soon</del>.