[BioC] marrayNorm to exprSet object

[Martin Morgan]

Hi Daniel --

Your work-around for adding geneNames to 'monkey' is the way to go --
here the problem is in the convert package, so perhaps the package
maintainer will incorporate a fix.

A featureNames method didn't exist for exprSet (it will in the next
release), so for now geneNames is the way to access the information
you want from an exprSet.

Martin

Daniel Brewer <daniel.brewer at icr.ac.uk> writes:

> Hello all,
>
> I am new to bioconductor and I am running into a couple of problems
> converting a marrayNorm object to an exprSet object.  I convert the
> marrayNorm object to an exprSet using the following:
>
> library("convert")
> xEset <- as(marrayNorm object, "exprSet")
>
> The problem is that there does not seem to be any probe level
> information in the exprSet i.e.
>> geneNames(monkey)
> NULL
>> featureNames(monkey)
> Error in featureNames(monkey) : no direct or inherited method for
> function 'featureNames' for this call
>
> This information is available in the marrayNorm object:
>> norm at maGnames@maInfo[1:10,]
>             ID     Name
> X22170   22170 DXF68S1E
> X21642   21642    ABCA2
> X22209   22209 LOC56990
> X22121   22121    PDZD2
> X24284   24284     PACE
> X66999   66999     CD74
> X110223 110223      DLD
> X110202 110202   EEF1A1
> X21744   21744     GGA2
> X22739   22739 FLJ14566
>
> I can fix the gene names by doing the following
>
> geneNames(monkey) <- norm at maGnames@maInfo$Name
>
> but the same does not work with the feature names.  Is the correct way
> to do this?  Anyway round the feature name problem.
>
> Many thanks
>
> Daniel Brewer
>
> -- 
> **************************************************************
>
> Daniel Brewer, Ph.D.
>
> Institute of Cancer Research
>
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