[BioC] Significant p-values disappear in limma

[michael watson (IAH-C)]

Hi

Sorry to labour the point, but following on from my last mail, I have
four arrays in a replicated dye swap experiment.  After carrying out the
analysis in limma, I find that 360 out of 4600 genes have an unadjusted
p-value <= 0.05.  However, when I adjust these using adjust="fdr", all
of these disappear, and I have p-values of 0.5 and upwards.  My B
statistics seem much lower than in other analyses I have done, even
though the t-statistics are still quite large, as are (some of) the M
and A values.  

I was just wondering if anyone had seen this before and could shed some
light on what this might say about my data.  When the top gene from
topTable() has log2 ratios of 4.11, 5.51, 3.53 and 4.3, yet has an
adjusted p-value of 0.2790644 and a B value of only 1.080982225, I
figure something must be badly wrong somewhere...

Thanks in advance

Mick