>>>>> "GS" == Gordon K Smyth <[EMAIL PROTECTED]> >>>>> on Sat, 8 Jan 2005 01:11:30 +1100 (EST) writes: <.............>
GS> p.adjust() unfortunately gives incorrect results when GS> 'p' includes NAs. The results from topTable are GS> correct. topTable() takes care to remove NAs before GS> passing the values to p.adjust(). There's at least one bug in p.adjust(): The "hommel" method currently does not work at all with NAs (and I have an uncommitted fix ready for this bug). OTOH, the current version of p.adjust() ``works'' with NA's, apart from Hommel's method, but by using "n = length(p)" in the correction formulae, i.e. *including* the NAs for determining sample size `n' {my fix to "hommel" would do this as well}. My question is what p.adjust() should do when there are NA's more generally, or more specifically which `n' to use in the correction formula. Your proposal amounts to ``drop NA's and forget about them till the very end'' (where they are wanted in the result), i.e., your sample size `n' would be sum(!is.na(p)) instead of length(p). To me it doesn't seem obvious that this setting "n = #{non-NA observations}" is desirable for all P-value adjustment methods. One argument for keeping ``n = #{all observations}'' at least for some correction methods is the following "continuity" one: If only a few ``irrelevant'' (let's say > 0.5) P-values are replaced by NA, the adjusted relevant small P-values shouldn't change much, ideally not at all. I'm really no scholar on this topic, but e.g. for "holm" I think I would want to keep ``full n'' because of the above continuity argument. BTW, for "fdr", I don't see a straightforward way to achieve the desired continuity. 5D Of course, p.adjust() could adopt the possibility of chosing how NA's should be treated e.g. by another argument ``use.na = TRUE/FALSE'' and hence allow both versions. Feedback very welcome, particularly from ``P-value experts'' ;-) Martin Maechler, ETH Zurich ______________________________________________ R-devel@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-devel