[Bioc-devel] eSet for aCGH data

Vosse, S.J. S.Vosse at vumc.nl
Fri Oct 5 14:44:25 CEST 2007

I guess it would indeed be easiest to define a separate eSet subclass
for the different 'stages' of aCGH data, being raw, normalized,
segmented, called and regions. For this the ExpressionSet class can be
used with virtually no changes, except for perhaps some methods. Or
perhaps a single class, with a slot to define the type of data contained
in the class and thus the way methods behave.

Vincent, how does your cghSet class differ from the ExpressionSet class,
and why?


-----Oorspronkelijk bericht-----
Van: Vincent Carey 525-2265 [mailto:stvjc at channing.harvard.edu] 
Verzonden: Thursday, October 04, 2007 16:14
Aan: Vosse, S.J.
CC: bioc-devel at stat.math.ethz.ch
Onderwerp: Re: [Bioc-devel] eSet for aCGH data

> Dear all,
> first let me thank Martin Morgan and James MacDonald for their answers
> to my question about the exprSet class on the Bioconductor mailing
> They have been very helpful.
> I am thinking to adapt/extend the eSet class or probably ExpressionSet
> to contain aCGH data for our package CGHcall. My question is whether a
> similar class for aCGH data already exists or if anyone has been
> on it or has thoughts on the subject. The class would be the same as
> ExpressionSet, only there would need to be slots for raw data,
> normalized data, segmented data, called data and regions data
> (http://la-press.com/cr_data/files/f_CIN-3-Wiel-et-al_96.pdf).

you might have a look at the Neve2006 package, only in the devel
experiment data branch (currently labeled 2.1 on the web site)

i did not push this package into release because of lack of consensus
on the preferred representation of aCGH data.  we have a number of
packages like aCGH, DNAcopy, snapCGH that use their own representations.

cghSet and cghExSet are defined in Neve2006.  cghExSet confronts the
problem of managing expression and CGH data obtained on the same

i question whether you should have a class that manages
raw and normalized and segmented data together.  we have used stagewise
representations in the expression domain, with containers like
for the raw intensities and ExpressionSet devoted to expression level
quantifications that will be analyzed downstream.  binding data together
at various levels of processing may have some benefits but also many
costs if the data are voluminous.

for what you mention, it seems that the normalized and/or called data
regions data would be in the AssayData and featureData eSet slots

once we get some consensus among multiple developers/users in place, it
is likely that a central eSet derivative class devoted to aCGH data
be defined in Biobase (or some relevant primarily core-maintained
for interested developers to use.

we can start a wiki page on the developer's wiki devoted to this topic
if there is sufficient interest
> Sjoerd Vosse
> 	[[alternative HTML version deleted]]
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