From smyth at wehi.edu.au  Tue Jan 18 01:32:10 2005
From: smyth at wehi.edu.au (Gordon Smyth)
Date: Tue Jan 18 01:34:08 2005
Subject: Fwd: Re: [Rd] p.adjust(<NA>s), was "Re: [BioC] limma and
  p-values"
Message-ID: <6.2.0.14.1.20050118112129.0214ca88@imaphost.wehi.edu.au>

On Sun, 16 Jan 2005 19:44:26 +1100, I wrote
>I can only think of one situation in which the NAs might represent unknown 
>but existing p-values. This would be when a large experiment has been 
>conducted leading to many p-values. Instead of inputing all the p-values 
>to the p.adjust() function, you decide to enter only the smallest p-values 
>and represent the others using NAs. The trouble with this approach is that 
>it can only be used with method="bonferroni".

Actually this could be done with "holm" as well as "bonferroni". Holm's 
method enforces monotonicity of the adjusted p-values by working up from 
the low end rather than working down from the high end, so just knowing the 
small ones is still ok.

Gordon

>  All the other adjustment methods are step-up or step-down methods or 
> involve closure like Hommel's method. For these methods, you simply have 
> to know all the p-values before you can adjust any of them.


Fwd: Re: [Rd] p.adjust(<NA>s), was "Re: [BioC] limma and p-values"
Gordon Smyth