Hi to all

I'd like to resolve this question:


in R 2.4 and bioconductor 1.9 I used the follow string to read my phenodata
in txt file (mysamplehe):
where "esetmysamples" is my dataset

# Reading and setting phenodata

> pd <- read.phenoData(filename="mysamplesphe.txt", sep="\t", header=TRUE)
> pData(esetmysamples)

and this to remove AFFX-id probes

### Removing AFFX-id probes

>ids <- (geneNames(esetmysamples))
>ids.affx <- grep("^AFFX", ids)
>ids.noaffx <- setdiff(c(1:length(ids)), ids.affx)
>esetmysamples <- esetmysamples[ids.noaffx,]

now, in R 2.5 and bioconductor 2.0 I must use read.'AnnotatedDataFrame'
instead of 'read.phenoData' and 'featureNames'  instead of

and here I have the Warning message:


> setwd(workdir)
> esetmysamples <- rma(mysamples)
Background correcting
Normalizing
Calculating Expression
> sampleNames(esetmysamples) <- smpls
>
> # Removing AFFX-id probes
> ids <- (geneNames(esetmysamples))
Warning message:
'geneNames' is deprecated.
Use 'featureNames' instead.
See help("Deprecated")
> ids.affx <- grep("^AFFX", ids)
> ids.noaffx <- setdiff(c(1:length(ids)), ids.affx)
> esetmysamples <- esetmysamples[ids.noaffx,]
> setwd(workdir)
> pd <- read.phenoData(filename="mysamplesphe.txt", sep="\t", header=TRUE)
Warning messages:
1: read.phenoData is deprecated, use read.AnnotatedDataFrame instead
2: The phenoData class is deprecated, use AnnotatedDataFrame (with
ExpressionSet) instead
> #esetmysamples <- new("exprSet", exprs = exprs(esetmysamples), phenoData =
pd)
> phenoData(esetmysamples) <- pd
Error in function (classes, fdef, mtable)  :
        unable to find an inherited method for function "phenoData<-", for
signature "ExpressionSet", "phenoData"
>

Can anyone help me to write the right the R.script?


thanks a lot

ardi

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