Question: deseq: all padj values equal to 1
0
gravatar for ccheung
4.7 years ago by
ccheung0
European Union
ccheung0 wrote:

Hi Everybody,

I performed a deseq analysis on my samples (11 controls and 33 experimental samples). It is true that there are huge variations within each group, but although the pval are very low, the padj are always 1.  Plus when I put in the command:

resSig = res[ res$padj <.05,]

the list that it gives me includes all the transcripts although the padj are 1.

I would really appreciate any advice or help. Thanx in advance.

 

carol

deseq padj • 1.8k views
ADD COMMENTlink modified 4.5 years ago by Michael Love25k • written 4.7 years ago by ccheung0

Please post the complete code that you used including some output to show snippets of the result tables, and maybe also the output of DESeq2' diagnostic plots.

And, in case you were using DESeq rather than DESeq2, please consider starting over with DESeq2. DESeq is outdated.

ADD REPLYlink written 4.7 years ago by Simon Anders3.6k
Answer: deseq: all padj values equal to 1
1
gravatar for Michael Love
4.5 years ago by
Michael Love25k
United States
Michael Love25k wrote:

This is just a natural consequence of the Benjamini Hochberg correction. It means none of the p-values were small enough to survive multiple test correction. Here's an example:

> p.adjust(c(.8,.9,1), method="BH")

[1] 1 1 1

 

 

ADD COMMENTlink written 4.5 years ago by Michael Love25k
Answer: deseq: all padj values equal to 1
0
gravatar for 15150688610
4.5 years ago by
China
151506886100 wrote:

Hello,I am encounting the same question with you.

Could you please tell that have you ever found out the reasons?

If so,could you please give me some advice.

ADD COMMENTlink written 4.5 years ago by 151506886100
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