[BioC] limma - paired design

[Naomi Altman]

Dear Mayra,
The variance estimator comes from doing an ANOVA with patient as 
block.  The t-tests you want are then done using contrasts.

--Naomi

At 04:24 AM 10/24/2007, Mayra Eduardoff wrote:
>Hi,
>I am having problems fitting the following model into limma, I have
>tried many different ways of specifying the design and contrast matrix
>but they all seem nonsense so I won t post them here, but maybe anyone
>knows how to properly fit this:
>
>I have data from 13 Patients, sampled at three different time points,
>0h (Control), 6h Treatment, 24h Treatment, so all in all 39 arrays and
>I want to do paired t tests for differential expression between 6h-0h
>and 24h-0h (not ! an ANOVA over both Time points). Until now we have
>been doing this fitting the model for the 6h and 24h separately, which
>works fine, but in oder to take all data into account for the mod. t
>tests variance estimator I guess i need to fit all data into one
>model.
>
>kind regards,
>
>Mayra
>
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Naomi S. Altman                                814-865-3791 (voice)
Associate Professor
Dept. of Statistics                              814-863-7114 (fax)
Penn State University                         814-865-1348 (Statistics)
University Park, PA 16802-2111