[BioC] limma, remove two type of batch effect

Fabrice Tourre fabrice.ciup at gmail.com
Tue Dec 28 13:21:04 CET 2010

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.

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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