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

 

 


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