adjusting p-value for GO analysis

Question

[milanlove]

how can i adjust p-values of GO analysis using bonferroni correction? it confused me for several days. it is possible using p.adjust function in R? i d'not know how to set n argument in this function

[milanlove]

DAVID tool gave a column named "bonferroni", is it corrected p-value?

[WouterDeCoster]

Please use ADD COMMENT or ADD REPLY to answer to previous reactions, as such this thread remains logically structured and easy to follow. I have now moved your post but as you can see it's not optimal. Adding an answer should only be used for providing a solution to the question asked.

Answer 1

[andrew.j.skelton73]

Read the manual

[milanlove]

i read it before you suggest it to me. my goal is select best way to it and also i want to know about n argument

[andrew.j.skelton73]

Have you looked at the example code they provide at the bottom?

Answer 2

[moxu]

use FDR correction. In R, use:

p.adjust(pval,  method="fdr", ...)