[BioC] S4 object??

[James W. MacDonald]

What is the output from sessionInfo(), and what do you get if you run 
traceback() right after the error?

Jim



Wendy Chen wrote:
> Hi Jim,
>  
> Even without creating the ExpressionSet I get the same error at the 
> lmFit step:
>  
> library(limma)
> library("Biobase")
> data <- read.table("c:/temp/data.txt",header=T,row.names=1)
> ExpressionData <- as.matrix(data[,c(2,3,4,6,7,8)])
> design <-cbind(WT=1,P=c(0,1,1,0,1,1),G=c(0,1,0,0,1,0))
> fit <-lmFit(eset,design)
> Error in possibleExtends(cl, class2, class1Def, class2Def) :
>     trying to get slot "subclasses" from an object (class 
> "classRepresentation") that is not an S4 object
>  
> I am suspecting I did not install something properly as I have done all 
> those commands before changing to a new computer and it all worked fine. 
> I have since tried re-installing everything but nothing works. Any idea 
> what does that error message mean?
>  
> Regards,
> Wendy
>  
> <http://punni3.blogspot.com/> 
> 
> 
> ------------------------------------------------------------------------
> *From:* James W. MacDonald <jmacdon at med.umich.edu>
> *To:* Wendy Chen <wenehc at yahoo.com.sg>
> *Cc:* bioconductor at stat.math.ethz.ch
> *Sent:* Thu, October 22, 2009 9:12:09 PM
> *Subject:* Re: [BioC] S4 object??
> 
> Hi Wendy,
> 
> Wendy Chen wrote:
>  > Hi all,
>  >
>  >
>  > I have loaded the LIMMA and Biobase package and tried these commands:
>  >
>  >
>  > library(limma) library("Biobase") data <-
>  > read.table("c:/temp/data.txt",header=T,row.names=1) ExpressionData <-
>  > as.matrix(data[,c(2,3,4,6,7,8)]) eset <- new("ExpressionSet", exprs =
>  > ExpressionData) design <-
>  > cbind(WT=1,P=c(0,1,1,0,1,1),G=c(0,1,0,0,1,0)) fit <-
>  > lmFit(eset,design)
>  >
>  > But I keep getting an eroor message after "lmFit" that says: Error in
>  > possibleExtends(cl, class2, class1Def, class2Def) : trying to get
>  > slot "subclasses" from an object (class "classRepresentation") that
>  > is not an S4 object
>  >
>  > I am using R-2.9.2. Whats happening now? I have done exactly the same
>  > commands in another computer and it works fine. I forgot which R
>  > version it was. But after installing the latest version nothing
>  > works. Pls advice...
> 
> I'm not sure why you get that error, but I would imagine it has 
> something to do with the ExpressionSet you are creating. Note that limma 
> will take any number of objects as input, including a matrix, so you 
> don't need to create an ExpressionSet anyway.
> 
> Usage:
> 
> 
> lmFit(object,design=NULL,ndups=1,spacing=1,block=NULL,correlation,weights=NULL,method="ls",...) 
> 
> 
> Arguments:
> 
>   object: object of class 'numeric', 'matrix', 'MAList', 'EList',
>           'marrayNorm', 'ExpressionSet' or 'PLMset' containing
>           log-ratios or log-values of expression for a series of
>           microarrays
> 
> Best,
> 
> Jim
> 
> 
> 
>  >
>  > Regards, Wendy
>  >
>  >
>  >
>  > [[alternative HTML version deleted]]
>  >
>  >
>  >
>  > ------------------------------------------------------------------------
>  >
>  >
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> -- James W. MacDonald, M.S.
> Biostatistician
> Douglas Lab
> University of Michigan
> Department of Human Genetics
> 5912 Buhl
> 1241 E. Catherine St.
> Ann Arbor MI 48109-5618
> 734-615-7826
> 

-- 
James W. MacDonald, M.S.
Biostatistician
Douglas Lab
University of Michigan
Department of Human Genetics
5912 Buhl
1241 E. Catherine St.
Ann Arbor MI 48109-5618
734-615-7826