Dear Aliaksei,
thank you for your help!

Stefano


On Fri, Jul 19, 2013 at 3:28 PM, Aliaksei Holik <salvador@bio.bsu.by> wrote:

> 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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>>
>>


-- 
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*He tried to be a scientist*

Stefano Capomaccio, PhD
Università Cattolica del Sacro Cuore
Via Emilia Parmense, 84
29122 - Piacenza (PC), Italy
Phone +39 0523 599203 (office)
Phone +39 0523 599482 (lab)
email: stefano.capomaccio@unicatt.it
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skype: capemaster

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