[BioC] reporterInfo for exprSet subsets

[Christos Hatzis]

Dear list,

I am not sure if this message was delivered before.  By checking the archive
I could not see body of the message, so here I am sending it again as plain
text.  My apologies if this has resulted in multiple postings. 

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/>