Hi,

 

Although I can't imagine I'm the first one to get the error message
unfortunately my gmane-searches were unsuccessful. When I apply limmas
lmFit() to an exprSet object I get the error message:

 

"Error in as.vector(x, mode) : cannot coerce to vector"

 

There is no problem using lmFit() with the expressionset table exprs(eset)!
According to the documentation it should be possible to directly use the
exprSet object. Here is an example code resulting in the error message with
me:

 

> library("ALL")

> library(limma)

> data("ALL")

> eset <- ALL[, ALL$mol.biol %in% c("BCR/ABL", "ALL1/AF4")]

> f <- factor(as.character(eset$mol.biol))

> design <- model.matrix(~f)

> fit <- eBayes(lmFit(eset,design))

 

--> Error in as.vector(x, mode) : cannot coerce to vector

 

As already mentioned the following command works ok:

 

> fit <- eBayes(lmFit(exprs(eset),design))

 

 

Has anyone observed the error before and if it is none then what am I doing
wrong?

 

regards,

 

Benjamin

 

 

Version numbers:

----------------

R: 2.4.0 under WinXP

Limma: 2.9.1

Biobase: 1.12.2

Tools: 2.4.0

ALL: 1.4.1

 


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