[BioC] Very low P-values in limma

Wolfgang Huber whuber at embl.de
Wed Oct 21 20:09:57 CEST 2009

Dear Paul

can you provide a more specific description of what you did than 
"analyzing ... data using limma"? The posting guide makes good suggestions.

There is a possibility that this is related to the eBayes procedure 
(which makes an assumption on the distribution of the within-group 
variances across the experiment). What is the value of the element 
"df.prior" of the object returned by eBayes?

Paul Geeleher ha scritto:
> 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.


Best wishes

Wolfgang Huber

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