[BioC] How to pool subgroups for makeContrasts() and subsequent limma analysis?

René rene.boettcher86 at gmail.com
Tue Feb 5 14:51:49 CET 2013


Hi James,

Thanks a lot for clarifying, now I can continue with my analysis.

Best regards,
René

> Hi René,
>
> On 1/23/2013 4:14 AM, René wrote:
>> Dear all,
>>
>> My current analysis revolves around various groups and their 
>> subgroups, which is why I would like to know how I can pool two or 
>> more subgroups in a contrast matrix.
>> As an example, let us assume I have 4 main groups (A, B, C and D), of 
>> which one can be subdivided into 3 subgroups (B1, B2 and B3), hence
>>
>> groups = c("A","B1","B2","B3","C","D")
>>
>> Now, I would like to compare the combined/pooled group B (consisting 
>> of B1, B2 and B3) against all other groups,
>>
>> B vs A, B vs C, B vs D.
>>
>> So my question is: how do I formalize that with makeContrasts() for 
>> an analysis with limma?
>> If it would be different matrices, I would just use cbind(), however 
>> I am not sure whether B1+B2+B3 does the same thing in makeContrasts().
>
> You are almost there. Note that you want the mean of the three groups, 
> not the sum. So
>
> makeContrasts((B1 + B2 + B3)/3 - A)
>
> will e.g., do the comparison of B vs A.
>
> Best,
>
> Jim
>
>
>>
>> Thank you in advance and best regards
>>
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>



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