[BioC] S4 object??

[James W. MacDonald]

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
> 
> 
> 
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> 
> 
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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