[BioC] Tools for Combining Affy and aCGH data

[Vincent Carey 525-2265]

I have introduced an experimental approach to the combination
of expression and CGH data in the Neve2006 package.  This is
available through the Browse packages/ExperimentData path
on the portal.  In the most recent devel version I introduce
a class called cghExSet that has AssayData components for
expression and logRatios, and accessors for both.  a
cloneMeta slot holds an annotated data frame that names and
indexes clone locations both on chromosomes and along entire
genome.

I say it is experimental because I don't have proven workflow
examples with it.  But it seems to differ from the available
CGH container designs in that it binds the sample level data
directly to the CGH assay results (and it differs
by keeping CGH and expression together).

It is unusual to push a class design in an experimental data
package but until I get comfortable with it I am keeping it
close to the data; the class definitions can be migrated to
Biobase (or some to-be-defined CGH infrastructure package)
if appropriate.  In fact I am not thrilled with the current
design that I have but the interface seems ok -- that is,
the [few] methods defined seem useful, and that is what we should
focus on -- what are the methods that we want to interrogate
this combination of data most thoroughly?  And then the class
definition can evolve to support those most efficiently.

Last issue: the expression data is readily annotated because
we know the platform (hgu133a) and its annotation; the clone
data is not so easy because except for a table provided with
the publication of the data to the web, i don't know the provenance
of the location assertions.  If there are manufactured clone sets
used for CGH perhaps we need annotation packages for them, but
I don't know how to pursue this.

---
Vince Carey, PhD
Assoc. Prof Med (Biostatistics)
Harvard Medical School
Channing Laboratory - ph 6175252265 fa 6177311541
181 Longwood Ave Boston MA 02115 USA
stvjc at channing.harvard.edu

On Mon, 9 Jul 2007, Benjamin Otto wrote:

> Hi Torun,

Like Sean I too don't know of any currently available package to do so.
However have a look at the following papers:

1. Stranger et. al.:
http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&db=PubMed&list_uids=17
289997

2. Spielman et. al.:
http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&db=PubMed&list_uids=17
206142

3. Chin et. al:
http://linkinghub.elsevier.com/retrieve/pii/S1535610806003151


Benjamin


======================================
Benjamin Otto
University Hospital Hamburg-Eppendorf
Institute For Clinical Chemistry
Martinistr. 52
D-20246 Hamburg

Tel.: +49 40 42803 1908
Fax.: +49 40 42803 4971
======================================


-----Ursprüngliche Nachricht-----
Von: bioconductor-bounces at stat.math.ethz.ch
[mailto:bioconductor-bounces at stat.math.ethz.ch] Im Auftrag von Sean Davis
Gesendet: Saturday, July 07, 2007 9:25 PM
An: Tarun Nayar
Cc: bioconductor at stat.math.ethz.ch
Betreff: Re: [BioC] Tools for Combining Affy and aCGH data

Tarun Nayar wrote:
> Hi,
>
> Are there any tools out there to combine/ compare Affy gene expression
> and aCGH data? A collaborator has 12 aCGH expts and 12 affy expression
> chips from the same biological samples. He's interested in seeing if
> regions of CN alteration correspond to differences in gene expression.
> We've taken a stab at writing our own program for this, now I'm
> wondering if there are any pre-made tools to do the same.
>

I don't know of R/bioc packages for doing this directly, but some version of
correlation between CGH measurements and gene expression measures is
probably useful.  You can use standard R commands to do this.  Within any
region of amplification, note that there will likely be only a portion (of
unknown quantity) of gene expression that is correlated with copy number.

Sean

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