Question

correction for multiple testing

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7.7 years ago

ashkan ▴ 160

Hi Guys,

after my analysis I have got 3000 genes and I have read counts for all of them in two condition. I want to compare two conditions. do you guys know how to get the p-values for comparison of two conditions (I have 3 columns ). I think I also have to correct for multiple testing? do you guys know how to do that?

Thanks

RNA-Seq • 2.5k views

ADD COMMENT • link updated 7.7 years ago by andrew.j.skelton73 6.5k • written 7.7 years ago by ashkan ▴ 160

score 2 · Answer 1 · 2016-08-22

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7.7 years ago

andrew.j.skelton73 6.5k

See DESeq2

ADD COMMENT • link 7.7 years ago by andrew.j.skelton73 6.5k

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I am now doing Differential expression analysis. just I want to compare them statistically.

ADD REPLY • link 7.7 years ago by ashkan ▴ 160

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Following the DESeq2 vignette is by far the best way for you to apply the correct statistics. If you're asking what kind of statistical test to use, then DESeq2 implements a Wald test, with Benjamin Hochberg multiple test correction (FDR)

ADD REPLY • link 7.7 years ago by andrew.j.skelton73 6.5k