[BioC] Is it possible to generate an ExpressionSet object that contain duplicate row names?

[Martin Morgan]

On 10/13/2011 01:52 AM, Tim Triche, Jr. wrote:
> rownames(myexprsunique) = make.unique(rownames(myexprsunique))
> myExpressionSet<- new("ExpressionSet", exprs = myexprsunique, phenoData =
> myphenoData, annotation = myannotation)
>
> This is more of an R question than a BioC question, and don't forget to make
> the phenoData row names unique too.

actually, Nuria was sent here from R-help ;) ExpressionSet row names are 
meant to be unique identifiers; store other identifiers in featureData, 
e.g.,

fData(myExpressionSet)[["MyIds"]] <- 'whatever'

or create a featureData instance (it's an AnnotatedDataFrame, like 
phenoData) in new("ExpressionSet", featureData=featureData)

Hope that helps,

Martin


>
>
> On Wed, Oct 12, 2011 at 11:59 PM,<nqueralt at clinic.ub.es>  wrote:
>
>> Dear all,
>>
>>
>>
>> I am facing the problem that comes up when an ExpressionSet object is
>> intended to be created parsing a matrix expression data with duplicate row
>> names:
>>
>>
>>
>>> try(myExpressionSet<- new("ExpressionSet", exprs = myexprsunique,
>> phenoData = myphenoData, annotation = myannotation, check.names=FALSE))
>>
>> Error in data.frame(numeric(n), row.names = nms) :
>>
>>   duplicate row.names: blu
>>
>>
>>
>> I was wondering if there exists a way to create this ExpressionSet object
>> although duplicate row names exist in the expression matrix data parsed?
>> Many thanks in advance.
>>
>>
>>
>> Kind regards,
>>
>>
>>
>> Núria
>>
>>
>>
>>
>>         [[alternative HTML version deleted]]
>>
>>
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>
>
>
>
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