[BioC] limma and Rank Products: comparison of the number of results

[Juan Carlos Oliveros]

Tom,

Thanks for your message. Your explanations about the differences between 
the two methods are very clear and will help us to understand our results.

Cheers,

Juan Carlos

Thomas Hampton wrote:
> I have used rank products ad limma head to head many times, so I think 
> I understand your question.
>
> I can imagine scenarios where limma would provide a longer list, but I 
> have not observed it myself.
>
> It is in many ways amazing that the two tests generate similar lists 
> at all, given the enormous
> difference in the way they go about selecting genes. Limma "cares" 
> quite a lot about within
> group variation, and can select genes with very small between group 
> differences as significant
> as long as within group variation is sufficiently small.  Genes with 
> smaller p values appear at the
> head of the list in limma, where genes with the largest fold 
> differences appear at the head of
> a RankProd list. The net of all this is that I believe you will find 
> that the two lists are not only different
> in length, but quite different in order. So whether "false prediction 
> rates" and "false discovery rates" are
> arguably similar or not, the two tests make rather different 
> assumptions which will ultimately drive the two
> estimates apart. I generally feel that "longer is better" when it 
> comes to gene lists, especially for pathway
> analysis, but I generally require a difference of 1.4 fold between 
> conditions before I get enthusiastic.
>
> Best,
>
>
> Tom
>
>
>
> T
> On Feb 17, 2010, at 9:10 AM, Juan Carlos Oliveros wrote:
>
>> Dear all
>>
>> When working with comparative experiment based on Affymetrix gene 
>> expression arrays I usually apply one of the following combination of 
>> methods:
>>
>> RMA + limma + FDR
>>
>> or
>>
>> RMA+ Rank Products
>> (rank products "Percentage of false prediction" values are supposed 
>> to be equivalent to FDR)
>>
>> Usually we obtain much more differentially expressed genes when using 
>> Rank Products than when using limma at the same FDR threshold.
>>
>> I wonder if in your case is the same. Do you obtain many more results 
>> with Rank Products than with limma at the same FDR cutoff?
>>
>> In a recent experiment we obtained the opposite (more results with 
>> limma) and I'd like to know your experience when using both methods 
>> regarding the number of results.
>>
>> best,
>>
>> Juan Carlos Oliveros, Ph.D.
>> CNB-CSIC, Madrid, Spain
>>
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>