what is the best p value cuttoff to select differentially expressed genes ?
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7.9 years ago
jack ▴ 950

Hi,

I have don gene differential expression analysis of RNA-seq data using Deseq2. it's report the list of the differentially expressed genes with Fold change, pvalue and adjasuted P-value.

I know that, I should stick with adjusted P-value. but:

  1. What is the good and trust able threshold for P-value?
  2. Why just looking at fold change can be misleading?
sequencing genomics software-error RNA-Seq • 4.9k views
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Entering edit mode
7.9 years ago
  1. 0.1 is a common threshold for adjusted p-values
  2. suppose you have an outlier or a lowly expressed gene such that the observed fold-change is questionable...

For 2, the reality is that DEseq2 moderates the fold-change, so this should then be a bit more useful. still, at the end of the day you're not just interested in the magnitude of change between group but also how reliable that is.

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thanks. but you don't think 0.1 is not very low threshould ? you mean 0.01 ?

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I meant 0.1, 0.01 would be overly restrictive for an adjusted p-value. Of course, the threshold you'd actually use is dependent on what you're doing downstream. If you're going to base an expensive clinical trial on the results, then you'd use a more restrictive threshold.

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