deseq: all padj values equal to 1
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ccheung • 0
@ccheung-7248
Last seen 9.1 years ago
European Union

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 • 4.6k views
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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 DESeq is outdated.

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@mikelove
Last seen 1 day ago
United States

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

 

 

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@15150688610-7694
Last seen 9.5 years ago
China

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.

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