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Question: pvalue of deseq2
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gravatar for ed_isfahani
17 months ago by
ed_isfahani0 wrote:

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

ADD COMMENTlink modified 17 months ago by Ryan C. Thompson7.0k • written 17 months ago by ed_isfahani0
2

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.

ADD REPLYlink written 17 months ago by Ryan C. Thompson7.0k

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

ADD REPLYlink written 17 months ago by Ryan C. Thompson7.0k

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? 

ADD REPLYlink written 17 months ago by ed_isfahani0
2
gravatar for Ryan C. Thompson
17 months ago by
The Scripps Research Institute, La Jolla, CA
Ryan C. Thompson7.0k wrote:

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.

ADD COMMENTlink modified 17 months ago • written 17 months ago by Ryan C. Thompson7.0k

thank you very much,I thought the normalization use for meta-analysis while it is used for NOIseq. do you know I can use  DESeq2 instead of  DESeq? as I said In the package it is mentioned DESeq or edgeR.

ADD REPLYlink written 17 months ago by ed_isfahani0
1

I'm not familiar with the metaseq package, so I can't tell you how to use it with DESeq2, but if all it needs is a vector of p-values for each gene, DESeq2 can certainly provide that. If you want to know how to use DESeq2 in general, it comes with a detailed manual.

ADD REPLYlink written 17 months ago by Ryan C. Thompson7.0k
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