[R] problem with creation of eSet

[Martin Morgan]

Hi Manisha -- this is a bioconductor package, so ask on the
Bioconductor mailing list. The 'exprSet' class is quite old, and has
been replaced by the 'ExpressionSet' class. Update your venison of R
and Bioconductor (http://bioconductor.org/download). Then evaluate the
commands

> library(Biobase)
> openVignette()

and read the first vignette 'Biobase - An introduction to Biobase and
ExpressionSets'.

Hope that helps,

Martin

"Manisha Brahmachary" <mb3058 at c2b2.columbia.edu> writes:

> 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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-- 
Martin Morgan
Computational Biology / Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N.
PO Box 19024 Seattle, WA 98109

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