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been replaced by the 'ExpressionSet' class.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" <[EMAIL PROTECTED]> 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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> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
--
Martin Morgan
Computational Biology / Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N.
PO Box 19024 Seattle, WA 98109
Location: Arnold Building M2 B169
Phone: (206) 667-2793
______________________________________________
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and provide commented, minimal, self-contained, reproducible code.
