Ryan C. Thompson | 21 May 04:45 2013

Re: Limma, model with several factors

Oops, I realized that subject only has 3 degrees of freedom, so as 
Gordon explained, you are perfectly fine blocking on subject.

On Mon May 20 09:44:28 2013, Ryan C. Thompson wrote:
> Ingrid,
>
> It is possible to block for any number of factors in limma. However,
> if you try to block for subject in the experiment that you showed, you
> will find that you don't have enough replicates to do so. The
> combination of treatment and timepoint contributes 4 degrees of
> freedom to your model, and subject would contribute 4 more, for a
> total of 8. This is the same as the number of samples in your
> experiment, which means that you have no remaining degrees of freedom.
> It would be analogous to trying to calculate the standard deviation of
> a single sample. Your best option is probably to block only for center
> and not subject.
>
> -Ryan
>
> On Mon May 20 01:01:08 2013, Ingrid Dahlman [guest] wrote:
>>
>> I have carefully read the Limma users guide but still have not sorted
>> out how I design the contrasts for the following Project.
>>
>> In want to compare the effect (After vs before) of two different
>> treatments, F and P. The study was carried our in two different
>> centers. This can be illustrated as follows:
>>   Subject center treatment timepoint
>>   1            1         F          B
>>   1            1         F          A
>>   2            1         P          B
>>   2            1         P          A
>>   3            2         F          B
>>   3            2         F          A
>>   4            2         P          B
>>   4            2         P          A
>>   I want to compare (F.A-F.B)-(P.A-P.B), blocking for subject.
>> However, in addition, I would like to block for center. I.e. the
>> center is like a batch effect.
>> Is it possible to block for two factors, suject and center, in the
>> same test in Limma?
>>   /Ingrid
>>
>>   -- output of sessionInfo():
>>
>> See section 8.7 in the user guide.
>>
>> --
>> Sent via the guest posting facility at bioconductor.org.
>>
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