[R] problem with creation of eSet

[James W. MacDonald]

Hi Manisha,

This is a Bioconductor-specific question. Please repost on the bioc 
listserv:

bioconductor at stat.math.ethz.ch

Best,

Jim



Manisha Brahmachary wrote:
> Hi,
> 
>  
> 
>  I am having troubles with creating an eSet and would appreciate any help on
> the following problem.
> 
>  
> 
> I am trying to create an eSet  using the following code 
> 
>  
> 
> pd <- read.table(file="pdata.txt",header =TRUE,row.names=1);
> 
> colnames(pd) <- c("type","tumor","time","id");
> 
> pdN <- list(type =
> "Cellline/xenograft",tumor="primary,secondary,cellline",time =
> "0hr,1hr,2hr,4hr", id = "1,2,3,4,5,6,7,8,9")
> 
> # Initialize exprSet object
> 
> pD <- new("phenoData", pData=pd, varLabels=pdN);
> 
> # This is my eSet!!!
> 
> metastasis.eset <- new("exprSet", exprs=as.matrix(geneExpr.log),
> phenoData=pD)
> 
>  
> 
> I get the following error:
> 
>  
> 
> The phenoData class is deprecated, use AnnotatedDataFrame (with
> ExpressionSet) instead
> 
>  
> 
>  
> 
> Can someone suggest me how to use the new method AnnotatedDataFrame to create
> eSet?
> 
>  
> 
>  
> 
> Thanks
> 
>  
> 
> Manisha
> 
>  
> 
>  
> 
> 
> 	[[alternative HTML version deleted]]
> 
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-- 
James W. MacDonald, M.S.
Biostatistician
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623