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

[john herbert]

Thanks James,
This does not have time course but judging by your answer, I can just
add this in, in place of, say, tissue.

Kind regards,

John.

On Thu, Oct 11, 2012 at 7:23 PM, James W. MacDonald <jmacdon at uw.edu> wrote:
> 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
>