[BioC] limma design experiment

[Gordon K Smyth]

Dear Luis,

I can't say.  Your description of your experiment was too brief for me to follow.

Best wishes
Gordon

> Date: Wed, 16 Mar 2011 18:55:50 -0400
> From: Luis Z <luisgls at gmail.com>
> To: bioconductor at r-project.org
> Subject: Re: [BioC] limma design experiment
>
> Dear Gordon,
>
> Thanks, I followed that already. My question is how can i treat each of my
> family samples as technical replicates and different family as a biological
> replicate. And if that is what you would suggest.
>
> Best,
>
> Luis Zapata
>
> On Wed, Mar 16, 2011 at 7:39 PM, Gordon K Smyth <smyth at wehi.edu.au> wrote:
>
>> Dear Luis,
>>
>> Are you asking how to construct a design matrix?  Why not
>>
>>  design <- modelMatrix(targets, ref="C")
>>
>> as described in the limma User's Guide?
>>
>> Best wishes
>> Gordon
>>
>>  Date: Tue, 15 Mar 2011 14:52:05 -0400
>>> From: Luis Z <luisgls at gmail.com>
>>> To: bioconductor at r-project.org
>>> Subject: [BioC] limma design experiment
>>> Message-ID:
>>>
>>> Hi everyone,
>>>
>>> I would like to receive a suggestion on the design model for this
>>> experiment.
>>>
>>> There are 5 different RNA pool families. Each one with three replicates
>>> (Technical?), coming from individuals that receive three different
>>> treatments, a control treatment and T1, T2. The experiment were made :
>>>                 fam    Cy3   Cy5
>>> slide 1         F1    T1   C
>>>                 F1    T1   C
>>>                 ....
>>>                 F5     T1   C
>>>                 F1     T2   C
>>>                 ...
>>>                 F5      T2   C
>>>
>>> What would you suggest?
>>>
>>> Thanks,
>>>
>>> Luis
>>> --
>>> Luis Zapata Ortiz
>>> Molecular Biotechnology Engineering
>>> Laboratory of Bioinformatics and Mathematics of the Genome, LBMG.
>>> Center of Mathematical Modeling of the University of Chile.
>>> Av. Blanco Encalada 2120
>>>  <56-2-9784551>56-2-9784551

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