[BioC] Limma; a kind of extended paired analyses with or without treatment
James W. MacDonald
jmacdon at uw.edu
Thu Oct 11 20:23:58 CEST 2012
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
> 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.
> Thank you.
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James W. MacDonald, M.S.
University of Washington
Environmental and Occupational Health Sciences
4225 Roosevelt Way NE, # 100
Seattle WA 98105-6099
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