[BioC] Very low P-values in limma

[Wei Shi]

Dear Paul:

    The low p-values you have got are not surprising to me. I have got 
even lower FDR adjusted p-values than yours. This just means you got 
significantly differentially expressed genes. But on the other hand, I 
did see much higher adjusted p-values in some of my microarray analyses. 
In that case, I will explore the data in more depth such as looking at 
batch effect etc.

Cheers,
Wei

Paul Geeleher wrote:
> Hi folks, I'm analyzing microRNA data using limma and I'm wondering about
> the validity of the p-values I'm getting out. Its a simple 'Group A Vs Group
> B' experimental design. 4 arrays in one group, 3 in the other and 4
> duplicate spots for each miRNA on each array.
>
> The lowest adjusted p-values in the differential expression analysis are in
> the region of 10^-7.
>
> Its been pointed out to me that plugging the point values from each sample
> into a regular t-test you get p=0.008, which then also needs to take the
> multiple test hit. Can anybody explain why limma is giving me such lower
> values and if they are valid?
>
> I can provide more information if required.
>
> Thanks,
>
> Paul.
>
>