Hi,

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? (https://github.com/mikelove/DESeq2).  I have not done much digging otherwise. 

Thanks,

Will

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."