[BioC] Significant p-values disappear in limma

[michael watson (IAH-C)]

Hi Sean

Unfortunately this one is out of my control (as usual), but I have much
smaller p-values with 4 arrays before, and even with 3 arrays.  Also
note that in one of my four-array experiments, EVERY single p-value was
0.9999963 after adjusting for the fdr - that's over 4600 spots, all with
the same p-value.  

Finally, note that the SWIRL dataset has only 4 arrays and limma
produces many, many p-values <= 0.05.

So, although I admit 4 arrays is far from ideal in terms of power,
something is nagging me that that's not it, and it certainly wouldn't
explain why over 4600 spots all have the same adjusted p-value - would
it?

Cheers
Mick  

-----Original Message-----
From: Sean Davis [mailto:sdavis2 at mail.nih.gov] 
Sent: 05 January 2005 12:49
To: michael watson (IAH-C)
Cc: bioconductor at stat.math.ethz.ch
Subject: Re: [BioC] Significant p-values disappear in limma


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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