[BioC] lmFit(eset,design) error message

[Benjamin Otto]

Gee, thanks Jim. I was worrying my "Documentation"-interpretation abilities
had suffered from the good weather period the last days here in hamburg. :-)

Regards,

Benjamin


-----Ursprüngliche Nachricht-----
Von: James W. MacDonald [mailto:jmacdon at med.umich.edu] 
Gesendet: 25 October 2006 17:10
An: Benjamin Otto
Cc: BioClist
Betreff: Re: [BioC] lmFit(eset,design) error message

Hi Benjamin,

I don't think you are doing anything wrong (other than calling an 
ExpressionSet an exprSet ;-D). The problem here is that lmFit() hasn't 
been updated to accept an ExpressionSet object, so it is erroring out.

As you note, lmFit() will accept a matrix, so if you extract the 
expression values into a matrix using the exprs() accessor, it will 
work. For now I think that is the best work-around.

Best,

Jim

Benjamin Otto wrote:
> 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
> 
>  
> 
> 
> 	[[alternative HTML version deleted]]
> 
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-- 
James W. MacDonald, M.S.
Biostatistician
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623


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