Hi Manisha,
This is a Bioconductor-specific question. Please repost on the bioc
listserv:
[EMAIL PROTECTED]
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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> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
--
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
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