difference between number of genes identified and pg matrix

[dachaotou]

Hi, Vadim
Im chao，i have a question for you. In the log.txt, Number of genes identified at 1% FDR: 3698 (precursor-level), 3173 (protein-level) (inference performed using proteotypic peptides only), this number is quite different with the pg matrix file which is more than 3173 and reach to 4900 protein groups.
i want to know why this two number is different and where can i find the list of Number of genes identified at 1% FDR,how this number count?

Thank you in advance!

Best,chao

[vdemichev]

Hi Chao,

Please see my last answer here #180.

Best,
Vadim

[vdemichev]

In short, there are two answers:
Super simple: if you are interested in gene groups, just use gg_matrix; if want unique genes, use the respective matrix
Also simple: use main report and filter either Global.PG.Q.Value <= 0.01 or GG.Q.Value <= 0.01

[dachaotou]

thanks a lot. problem solved.