R help - Oct 2009 - S4 object??

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...
 
Regards,
Wendy


      
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1. You forgot to give a *reproducible* example as the posting guide asks 
you to do.
2. Both packages you mentioned are BioConductor packages. Note that the 
BioConductor project has its own mailing list.

Best wishes,
Uwe Ligges



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...
>  
> Regards,
> Wendy
> 
> 
>       
> 	[[alternative HTML version deleted]]
> 
> 
> 
> ------------------------------------------------------------------------
> 
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