[BioC] Doubt on time course design

[Aliaksei Holik]

Oops. Too quick off the mark there. After replying I realised that you'd 
want to block the subject variable. And in that case your design matrix 
seems correct.

Sorry for replying without thinking :)

On 19/07/2013 23:13, Aliaksei Holik wrote:
> Dear Stephano,
>
> Unless you are looking for differential gene expression between subjects
> my suggestion would be:
>
> designMatrix <- model.matrix(~timepoints)
>
> OR
>
> designMatrix <- model.matrix(~0+timepoints)
>
> Depending on whether or not you wish to include the intercept term.
>
> Hope it helps,
>
> Aliaksei.
>
> On 19/07/2013 20:01, Stefano Capomaccio [guest] wrote:
>>
>> I'm writing because I have a doubt on how to perform a DGE analysis
>> with edgeR.
>> I followed both the tutorial and some interenet posts, but I got
>> confused and I'm not sure on how to properly account for variation
>> between individuals in my experimental design that is the following:
>>
>> RNA-Seq data of 6 subjects at 4 different time points (24 obs). There
>> is no control/treatment.
>> My goal is to reveal genes that are differentially expressed between
>> the time points.
>>
>> Should I design the matrix as follows?
>>
>> designMatrix <- model.matrix(~subjects+timepoints)
>>
>> Or there is something that I misinterpret?
>> Any advices on this issue?
>>
>> Thank you all for your cooperation.
>>
>>   -- output of sessionInfo():
>>
>> ...
>>
>> --
>> Sent via the guest posting facility at bioconductor.org.
>>
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>>
>
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