wouldn't it help to do

design <- model.matrix( ~ 0 + factor(AvsB) +
                              factor(gender) +
                              factor(pBatch),
                       data=pData(mldat.norm))

and then carry on?  It looks like you're trying to reference something that
ain't defined



On Tue, Dec 28, 2010 at 4:21 AM, Fabrice Tourre <fabrice.ciup@gmail.com>wrote:

> Hi All,
>
> In my analysis, I want to find the different expression genes between
> dissese A and B. There are two type of batch effect in my analysis. I
> want to use limma to remove two type of batch effect, one is gender,
> another is tissue type. I do as fellow. But I got a error. Is there
> some problem in my analysis? Thank you very much in advance.
>
>
> design<-model.matrix(~0+factor(pData(mldat.norm)$AvsB)+factor(pData(mldat.norm)$gender)+factor(pBatch))
> colnames(design) <- c("group1","group2","Sexbatch","pBatch")
>
> fit1 <- lmFit(exprs(mldat.norm),design)
> Coefficients not estimable: pBatch
> Warning message:
> Partial NA coefficients for 29198 probe(s)
>
> contrast.matrix <- makeContrasts(group2-group1,levels=design)
> fit2 <- contrasts.fit(fit1, contrast.matrix)
> fit2 <- eBayes(fit2)
> topTable(fit2, coef=1,adjust="BH",sort.by="P")
>
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>



-- 
If people do not believe that mathematics is simple, it is only because they
do not realize how complicated life is.
John von Neumann<http://www-groups.dcs.st-and.ac.uk/~history/Biographies/Von_Neumann.html>

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