[BioC] limma, remove two type of batch effect

[Fabrice Tourre]

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")