[BioC] error creating new exprSet

Seth Falcon sfalcon at fhcrc.org
Fri Jun 16 16:15:14 CEST 2006

Peter <bioconductor-mailinglist at maubp.freeserve.co.uk> writes:
> If you don't have any real phenotype data, then this will generate a 
> dummy phenotype object with the sample number:
> pheno <- read.phenoData(NULL, colnames(data), FALSE)
> good.eset <- new("exprSet", exprs=good, phenoData=pheno)
> The resulting phenotype data is just a "sample number" (i.e. column 
> number in the data matrix/array).

One of the main ideas of the exprSet class is to organize expression
values _and_ sample data (phenotype info).  In other words, I don't
think the common case is one in which there is no phenotype data other
than an ID.  

As you have found, the case of ID only can be handled by the current
code.  If there are others who would find such a default useful,
please speak up, otherwise I would suggest a smaller helper function
to create new exprSet instances for your particular use case.


+ seth

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