correction for multiple testing

Question

[ashkan]

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

Answer 1

[andrew.j.skelton73]

See DESeq2

[ashkan]

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

[andrew.j.skelton73]

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)