On Thu, Oct 22, 2009 at 9:27 AM, Wendy Chen <wenehc@yahoo.com.sg> 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)
>
>
You are still using "eset".  You want to use:

fit <- lmFit(ExpressionData,design)

Sean



> 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
>
>
>
>
>
>
> ________________________________
> From: James W. MacDonald <jmacdon@med.umich.edu>
>
> Cc: bioconductor@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]]
> >
> >
> >
> > ------------------------------------------------------------------------
> >
> >
> > _______________________________________________ Bioconductor mailing
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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
>
>
>
>
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