[BioC] adjusted p-values for large number of genes...

[Lourdes Peña Castillo]

Hello,

I am using  limma to select differentially expressed genes. I have 24
arrays and 40k genes. According to the limma users' guide, "If none of
the raw p-value are less than 1/G, where G is the number of genes,
then all of the adjusted p-values will be
equal to 1". 

I get raw p-values which are less than 1/G after applying eBayes;
however, the lowest adjusted p-value I get using "fdr"  is 0.66. Does
that mean that I cannot adjust for multiple testing in experiments
involving  many genes?   Should I then use an arbitrary cut-off on the
raw p-values? or what are the alternatives?

Thanks!

Lourdes