[BioC] limma - paired design

[Mayra Eduardoff]

Dear Naomi,

Thanks for your reply, can I then do it like this somehow:

data is my expressionSet containing all 39 Arrays, first 0h then 6h
then 24h always the same order of samples.

> block <- rep(1:13,3)
> design <- cbind(c(rep(1,13),rep(0,26)), c(rep(0,13),rep(1,13),rep(0,13)), > c(rep(0,26),rep(1,13)))
> rownames(design) <- c("0h","6h","24")

I ram not quite sure what this line does, as I don't understand what
the correlation parameter expects in my case, but it comes from an
example.

dupcor <- duplicateCorrelation(exprs(data),design,block=block)


> fit <- lmFit(exprs(data),design=design, block=block, correlation= dupcor$consensus)
> cont.wt <- makeContrasts("6h-0h","24h-0h", levels=design)
> fit2<- contrasts.fit(fit,cont.wt)



kind regards,
Mayra




On 10/24/07, Naomi Altman <naomi at stat.psu.edu> wrote:
> 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
>
>