[BioC] questions on results from mt.maxT (multtest)

[Straubhaar, Juerg]

Im am using R version 2.0.1, multtest version 1.5.2.

Microarray experiment: wildtype tissue vs KO tissue; affy MOE430_2
Experiments in triplicates.

ExprSet at exprs matrix has dimension: 45101 6

I used nonspecific filtering which reduces the number of genes to 1815 (exprSub)

I am using multtest to get a set of differentially expressed genes:

resT <-mt.maxT(exprSub at exprs, c(0,1,0,1,0))
This runs 20 permutations (complete enumeration)

sort(resT$rawp) looks like this:

[1] 0.1 0.1 0.1 0.1 0.1 0.1 0.1 0.1 0.1 0.1 0.1 0.1 0.1 0.1 0.1 0.1 0.1 0.1 0.1
[20] 0.1 0.1 0.1 0.1 0.1 0.1 0.1 0.1 0.1 0.1 0.1 0.1 0.1 0.1 0.1 0.1 0.1 0.1 0.1
[39] 0.1 0.1 0.1 0.1 0.1 0.1 0.1 0.1 0.1 0.1 0.1 0.1
...
[1711] 0.9 0.9 0.9 0.9 0.9 0.9 0.9 0.9 0.9 0.9 0.9 0.9 0.9 0.9 0.9 0.9 0.9 0.9
[1729] 0.9 0.9 0.9 0.9 0.9 0.9 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0
[1747] 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0
[1765] 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0
[1783] 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0
[1801] 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0

It looks like these p-values are rounded to one decimal digit. From these results none of the 1815  genes are differentially expressed between WT and KO, which is not quite believable. I would like to get p-values precise to several digits. Maybe there is something else I don't understand.

getOption('digits') 7

Thank you.

Juerg Straubhaar
Umass Med