[BioC] Significant p-values disappear in limma

[Sean Davis]

It seems that with only two experiments (with accompanying dye-swaps), 
it is certainly possible that you don't have enough power to detect a 
difference.  Can you do more experiments?

Sean

On Jan 5, 2005, at 6:58 AM, michael watson ((IAH-C)) wrote:

> 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
>
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