Hello,
I'm working with R 2.2.1 and BioC 1.7 and checked the following also in the Sources of genefilter 1.9.6 in BioC 1.8 Devel.
The function checkfac which occurs in rowttests (and colttests, ...) has only one argument "fac" but inside one calls ncol(x) if "fac" is missing.
This leads to the following wrong behavior (example from rowttests help page slightly modified)
x  = matrix(runif(960), ncol=96)
y = matrix(runif(970), ncol=97)
rowttests(y)
Which gives:
Fehler in rowttests(y) : length(fac)=96, ncol(x)=97, should be the same.
or 
rm(x)
y = matrix(runif(970), ncol=97)
rowttests(y)
Fehler: objekt "x" nicht gefunden
Fehler in ncol(x) : unable to find the argument 'x' in selecting a method for function 'ncol'
Best,
Matthias
 

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