[BioC] Limma; a kind of extended paired analyses with or without treatment

[James W. MacDonald]

Hi John,

On 10/11/2012 2:15 PM, john herbert wrote:
> Dear all.
> I have been pondering about constructing a design matrix based on the
> Limma user guide, where I combine a time course with a paired
> analyses. The targets file looks like;
>
> Sample	treatment	time
> 1	control	24
> 1	control	72
> 1	control	0
> 1	treatment	24
> 1	treatment	72
> 2	control	24
> 2	control	72
> 2	control	0
> 2	treatment	24
> 2	treatment	72
> 3	control	24
> 3	control	72
> 3	control	0
> 3	treatment	24
> 3	treatment	72
>
> Sample number refers to an individuals cancer cells, treatment refers
> to added drug or not and numbers are in hours (time elapsed). So it is
> a kind of paired, as patient variability is to be considered. The
> control sample at 0 is the same as treatment at time 0 as these are
> the same cells without any time/treatment.
>
> Please could someone help me understand how I can construct a design
> matrix and to understand how I can extract differently expressed genes
> that come about due to time, due to treatment and interaction of them
> both.
>
> Any pointers appreciated, though I am trying to see if the examples in
> the manual can be applied to this scenario.

See the multi-level experiment example in the user guide, starting on p. 47.

Best,

Jim

>
> Thank you.
>
> John.
>
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-- 
James W. MacDonald, M.S.
Biostatistician
University of Washington
Environmental and Occupational Health Sciences
4225 Roosevelt Way NE, # 100
Seattle WA 98105-6099