Gordon Smyth
2005-Jan-18 01:34 UTC
Fwd: Re: [Rd] p.adjust(<NA>s), was "Re: [BioC] limma and p-values"
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.