Question: DESEQ2 Default Value for Cooks Distance cutoff
gravatar for wpoehlm
4 months ago by
wpoehlm0 wrote:



I am using version 1.16.1 of DESeq2.  According to the documentation, a Cook's distance cutoff of 0.99 is applied to the results function by default.  I looked at the source code in github and this certainly seems to be the case.  However, if I get a larger number of significant genes when running the "results" function with default arguments compared to when I explicitly use the argument "cooksCutoff = 0.99".  Is version 1.16.1 in Bioconductor up to date with the source code on github? (  I have not done much digging otherwise. 





ADD COMMENTlink modified 4 months ago by Michael Love20k • written 4 months ago by wpoehlm0

Update: I updated to version 1.20.0 and I am noticing the same thing

ADD REPLYlink modified 4 months ago • written 4 months ago by wpoehlm0
gravatar for Michael Love
4 months ago by
Michael Love20k
United States
Michael Love20k wrote:

The default value for Cook's distance is not 0.99. From the help page for ?results:

"cooksCutoff : theshold on Cook’s distance, such that if one or more samples for a row have a distance higher, the p-value for the row is set to NA. The default cutoff is the .99 quantile of the F(p, m-p) distribution, where p is the number of coefficients being fitted and m is the number of samples."

ADD COMMENTlink written 4 months ago by Michael Love20k
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