hello all,

I want to use p-value of DESeq2 for meta-analysis,I want to know p-value of DESeq2 are normalize?if yes which method DESeq2 use for normalize?

I appreciate your help

pvalue of deseq2

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ed_isfahani
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@ed_isfahani-12190
Last seen 6.9 years ago

hello all,

I want to use p-value of DESeq2 for meta-analysis,I want to know p-value of DESeq2 are normalize?if yes which method DESeq2 use for normalize?

I appreciate your help

2

Entering edit mode

The normalization options are not for normalizing the p-values, they are for normalizing the RNA-seq data that is input into NOISeq. This option is not needed for DESeq2 or edgeR because both methods already implement their own normalizations. In fact, TMM is the edgeR normalization method. So if you are following the DESeq2 or edgeR manuals, the p-values that you get from these methods should already be computed using the appropriate normalization.

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When you posted this question, you misspelled the metaseq tag. I've fixed the spelling, which should improve the chances that the authors of that package will see it.

You're going to have to explain what you mean by normalizing p-values. Are you talking about corrections for multiple testing?

actually I have 5 experiment of RNAseq data. I want to do meta-analysis by metaseq package. this packag have two method for doing meta-analysis,one work by expression value which calculate noiseq and another work by p-value of deseq or edgeR.

when we work with noiseq method, in its function we can choose different method of normalization (tmm,rpkm,no normalization),but for p-value method there is not this opyion,I want to know why?