Question

adjusting p-value for GO analysis

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6.7 years ago

milanlove • 0

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

GO gene • 2.9k views

ADD COMMENT • link updated 6.7 years ago by moxu ▴ 510 • written 6.7 years ago by milanlove • 0

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

ADD REPLY • link 6.7 years ago by milanlove • 0

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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.

ADD REPLY • link 6.7 years ago by WouterDeCoster 47k

score 2 · Answer 1 · 2017-07-27

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6.7 years ago

andrew.j.skelton73 6.5k

Read the manual

ADD COMMENT • link 6.7 years ago by andrew.j.skelton73 6.5k

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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

ADD REPLY • link 6.7 years ago by milanlove • 0

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

ADD REPLY • link 6.7 years ago by andrew.j.skelton73 6.5k

score 1 · Answer 2 · 2017-07-27

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6.7 years ago

moxu ▴ 510

use FDR correction. In R, use:

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

ADD COMMENT • link 6.7 years ago by moxu ▴ 510