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=""/>
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=""/>
>
>
>
> [[alternative HTML version deleted]]
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
