[BioC] expression set objects

[Vincent Carey]

what is your sessionInfo() result?

On Thu, Jan 13, 2011 at 10:58 PM, Peevi Ijkl <ipeevi at yahoo.com> wrote:
> Hi list..
> I am trying to create an expression set object..here is what i did so far..
>
> pd <- read.AnnotatedDataFrame( "target.txt", header=T, row.names=1, sep=";" )
> pData(pd)
> expression_data <- ReadAffy( filenames = rownames (pData(pd)) )
> expression_data
> rma_expression_data <-rma(expression_data)
> rma_data <- exprs(rma_expression_data)
>
> now i want to create an expression set object from the above using the
> following:
> ALLSet <- new("ExpressionSet", exprs =rma_data, phenoData = pd,
> + annotation = "hgu95av2")
> but I am getting the following error when i use the above
>
> Error in validObject(.Object) :
>  invalid class "ExpressionSet" object: 1: row numbers differ for assayData
> members
> invalid class "ExpressionSet" object: 2: sample numbers differ for assayData
> members
>
> while if i use rma_expression_data at the highlighted area am getting the
> following error:
> Error in function (classes, fdef, mtable)  :
>  unable to find an inherited method for function "annotatedDataFrameFrom", for
> signature "ExpressionSet"
>
> any help would be appreciated.
>
> thanks
> peevi
>
>
>
>
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