[BioC] S4 object??

[Martin Morgan]

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-- 
Martin Morgan

On Oct 22, 2009, at 5:25 PM, Wendy Chen <wenehc at yahoo.com.sg> wrote:

>> From sessionInfo() and traceback(), I get
>
>> sessionInfo()
> R version 2.9.2 (2009-08-24)
> i386-pc-mingw32
> locale:
> LC_COLLATE=English_United States.1252;LC_CTYPE=English_United States. 
> 1252;LC_MONETARY=English_United States. 
> 1252;LC_NUMERIC=C;LC_TIME=English_United States.1252
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
> other attached packages:
> [1] limma_1.9.0   Biobase_2.4.1
>> traceback()
> No traceback available
>
>
>
>
>
>
>
> ________________________________
> From: James W. MacDonald <jmacdon at med.umich.edu>
>
> Cc: bioconductor at stat.math.ethz.ch
> Sent: Thu, October 22, 2009 9:31:24 PM
> Subject: Re: [BioC] S4 object??
>
> 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>
>
>> *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]]
>>   >
>>   >
>>   >
>>   >  
>> --- 
>> ---------------------------------------------------------------------
>>   >
>>   >
>>   > _______________________________________________ Bioconductor  
>> mailing
>>   > list Bioconductor at stat.math.ethz.ch <mailto:Bioconductor at stat.math.ethz.ch 
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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
>
>
>
>
>    [[alternative HTML version deleted]]
>
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