Entering edit mode
11.4 years ago
xiaoqiaoliu
•
0
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.
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>.