[R] edgeR: design matrix setup

[Martin Morgan]

On 05/23/2012 07:24 AM, rmje wrote:
> I have a data frame like this:
>
>                         T0h T0.25h T0.5h  T1h  T2h  T3h  T6h T12h T24h T48h
> C0h C0.25h C0.5h  C1h  C2h  C3h  C6h C12h C24h C48h
> NM_001001130   68     95    56   43   66   62   68   90   63   89   65
> 85    58   49 81   49   76   73   48   77
> NM_001001152   79    129    52   50   24   45  130  154  112  147   56
> 85    67   33 52   31   93   77   65  109
> ...
> ...
> ...
>
>
> It has about 29000 rows and 20 columns (incl col.name).
> How would you set this up in edgeR if you want to compare the 10 first with
> the 10 last?

Please ask questions about Bioconductor packages on the Bioconductor 
mailing list

   http://bioconductor.org/help/mailing-list/

There have been recent time-course questions on the mailing list, so 
it's good to browse recents posts. Remember to include sessionInfo(). 
Have you looked at the extensive vignette for this package

   http://bioconductor.org/packages/2.10/bioc/html/edgeR.html

and limma, and taken a stab at answering your own question? It helps to 
see where you're coming from...; for this particular question and if 
you're statistically naive it might help to have a conversation with 
someone local who is a little versed in statistics.

Martin

>
>
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