[BioC] p-value adjustment

[Gordon Smyth]

>Wenbin Liu wnbnl at yahoo.com
>Wed Mar 23 23:51:28 CET 2005
>
>Dear list,
>
>I'm puzzled by the R function p.adjust with NA values
>in the first argument. The adjustment gives different
>result with and without the NAs.

Please refer to the extensive recent discussion on this topic on the 
R-devel mailing list.

>  The question then is,
>which approach should one take: with or without NAs in
>the first argument?

The limma package functions remove NAs before using p.adjust(), and I 
believe this is virtually always correct in the microarray context.

Gordon

>Thanks a lot!
>
>Wenbin