Question: what is the best p value cuttoff to select differentially expressed genes ?
gravatar for jack
4.3 years ago by
jack750 wrote:



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 ?

ADD COMMENTlink modified 4.3 years ago by Devon Ryan89k • written 4.3 years ago by jack750
gravatar for Devon Ryan
4.3 years ago by
Devon Ryan89k
Freiburg, Germany
Devon Ryan89k wrote:
  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.

ADD COMMENTlink written 4.3 years ago by Devon Ryan89k

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

ADD REPLYlink written 4.3 years ago by jack750

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.

ADD REPLYlink written 4.3 years ago by Devon Ryan89k
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