Hello,

I realized that the decideTests function in limma selects as differentially expressed only genes whose p-value is less than an alpha threshold, rather than those that are less than or equal to alpha. Taking this to an extreme case, when alpha = 1, some genes are still not selected as differentially expressed. Is there a reason for this? Would it make sense to add a parameter to the function to define whether the alpha threshold is inclusive or exclusive (with default maybe being inclusive)?

Thank you for your suggestions!

Best,

Roberto

If you reinstall limma, you will find that decideTests() was modified a few months ago so that it does in fact select genes with p-values less than or equal to the specified level. Here is a simple example that you can run for yourself:

> example(lmFit)
> summary(decideTests(fit2,p=1))
   Grp1 Grp2vs1
-1   52      52
0     0       0
1    48      48

As you can see, all genes are DE.

However I have never seen a data example for which "<" vs "<=" would make any difference except for p=1. It is very unlikely indeed that a p-value would be exactly equal to 0.05, or any other specified value, in floating point arithmetic. So I don't see a compelling reason to offer options in this regard.