[BioC] Doubt on time course design

[Aliaksei Holik]

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.
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at r-project.org
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
>
>