[BioC] reporterInfo for exprSet subsets

[Martin Morgan]

Thanks Christos for spotting this. The development version of Biobase
now subsets reporterInfo in a consistent way. Valid eSet and exprSet
objects must either have no reporterInfo/reporterNames, or information
on the same number of reporters as there are genes.

Martin

"Christos Hatzis" <christos at nuverabio.com> writes:

> Dear list,
>  
> I have been working with the exprSet class to manage analyses across several
> large datasets.  I have found the class to be extremely useful and a very
> efficient way for compactly organizing information on both the samples
> through the pData slot and the genes through the reporterInfo slot.
>  
> The subset operators work consistently to subset exprSet object based on
> subsets genes or samples.  However, it appears that there is an
> inconsistency in the way the reporterInfo data frame is treated.  Although
> selecting subsets of samples operates both on the expression matrix and the
> pData, subset selection on genes operates only on the expression matrix and
> not on the reporterInfo dataframe.  I would think that for consistency, the
> gene-based subset operator should also appropriately subset the reporterInfo
> data frame, since the remaining genes are not really relevant to the new
> object.
>  
> Is this a bug or is it rather the desired behavior?  I would appreciate any
> insight.
>  
> Thank you.  
>  
> Christos Hatzis, Ph.D.
> Vice President, Technology
> Nuvera Biosciences, Inc.
> 400 West Cummings Park
> Suite 5350
> Woburn, MA 01801
> Tel: 781-938-3830
> www.nuverabio.com <http://www.nuverabio.com/> 
>  
>  
>
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