Dear all,

I was trying to make expression set from the GSE data

Following is the code

gse6901 <- getGEO("GSE6901", GSEMatrix=F)
probesets <- Table(GPLList(gse6901)[[1]])$ID
data.matrix <- log2(do.call("cbind", lapply(GSMList(gse6901), function(x) {
+ tab <- Table(x)
+ mymatch <- match(probesets, tab$ID_REF)
+ return(as.numeric(tab$VALUE[mymatch]))
+ })))
rownames(data.matrix) <- probesets
colnames(data.matrix) <- names(GSMList(gse6901))
pdata <- data.frame(samples = names(GSMList(gse6901)))
rownames(pdata) <- names(GSMList(gse6901))
pheno <- new("phenoData", pData = pdata, varLabels = as.list("samples"))


Error: The phenoData class is defunct, use AnnotatedDataFrame (with
ExpressionSet) instead

I am not able to understand what function has exactly gor changed in Biobase
module as I tried

pheno <- new("AnnotatedDataFrame", pData = pdata, varLabels =
as.list("samples"))

then again got an error

Error in .nextMethod(.Object, ...) :
  invalid names for slots of class "AnnotatedDataFrame": pData, varLabels

Kindly anyone please help me sorting out this error, I shall be very
thankful for your kind help

Regards
-- 
Hemant Ritturaj Kushwaha

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