[BioC] Affy Exon Array Analysis

[Justin Borevitz]

Yes this one limitation, the annotation for new arrays.  So far we have done
our own and can share with other Arabidopsis people if there is interest.
We have developed methods for SFP (polymorphism detection)
http://naturalvariation.org/sfp
http://naturalvariation.org/methods
and are toying with novel gene prediction. Novel gene prediction is a
crucial area.  I'd like to hear others approaches toward it. Hidden markov
models are something we have been thinking of. Antisense expression is
another related and open area when strand specific expression is available.
Chip/chip and methylome analysis are others.  I expect methods to come out
in the next year as the arrays become more widely available.
http://naturalsystems.org/BorevitzEckerAnnualReview.pdf 
 
-----
Justin Borevitz

> -----Original Message-----
> From: Thomas Girke [mailto:thomas.girke at ucr.edu]
> Sent: Thursday, October 20, 2005 12:51 PM
> To: Justin Borevitz
> Subject: Re: [BioC] Affy Exon Array Analysis
> 
> Dear Justin,
> 
> Are there any BioC annotation packages (metadata) available for the
> Affy tiling arrays? If not could you explain how you performed the
> primary data analysis in R starting from cel files?
> 
> A more general question to the mailing list: what type of BioC anlaysis
> tools are currently under development to deal with the many additional
> data outputs from tiling arrays, e.g. mutant analysis, SNP and novel
> gene detection, etc.
> 
> Thanks for posting this info.
> 
> Thomas
> 
> 
> 
> On Thu 10/20/05 08:24, Justin Borevitz wrote:
> > Hi Reinhard and BioC
> > We've been using affy tiling arrays in Arabidopsis for alternative
> splicing.
> > The method is straight forward once exons or transcription subunits
> (parts
> > of known alternative exons) are defined.  We first look for differential
> > gene expression according to the treatment, time or your contrast.  Use
> your
> > favorite package, limma, siggenes etc.  Take the residuals from the
> model.
> > Now all genes have been corrected for alternative expression, look again
> at
> > the contrast for alternative transcription subunits, using your favorite
> > method.  In our case its about 25k genes and 120k subunits tested for
> > alternative splicing.  The key is one is limited to get an idea for
> > alternative splicing within a gene in a single condition given the large
> > variance in probe effects, what does that mean biologically anyhow.
> What
> > one has power for is alternative splicing across conditions.
> >
> > Finally there is a semantic argument to be made, what does alternative
> gene
> > expression mean if there is alternative splicing? One could put both
> gene
> > expression and splicing in a single model, here though one exon would
> have
> > to be a reference, others are tested for an exon:treatment interaction
> > effect.  If that reference exon was alternatively spliced, it would be
> taken
> > as the gene expression difference and all the other exons alternatively
> > spliced.  Any how I just like to fit the models separately, its easier
> to
> > think about and explain.  Gene expression is difference in overall means
> > using all probes(exons). Alternative splicing is a difference across
> probes
> > in a subunit.
> >
> > Hope it helps.. We can provide code but it's in a format for tiling
> arrays
> > not yet an affybatch
> > Justin
> > -----
> > Justin Borevitz
> > Ecology and Evolution (CLSC 915E)
> > University of Chicago
> > 1101 E. 57th St.
> > Chicago, IL 60637 USA
> > (773) 702-5948 office
> > (773) 834-4055 lab
> > borevitz at uchicago.edu
> > http://naturalvariation.org
> >
> > _____________________________
> > Dear Group,
> > Affymetrix recently launched arrays for exon analysis, containing
> > approx. 1.4 million probe sets. Athough some methods for detection of
> > alternative splicing events (MIDAS, PAC) have been described in
> > Affymetrix White Papers, these algorithms do not seem to be
> > implemented anywhere.
> > Does anybody have these or other tools for the analysis of Affyon
> > arrays (detection of alternative splicing events) available, maybe as
> > R code or so? Any help would be greatly appreciated.
> > Sincerely Reinhard
> >
> > --
> > Dr. Reinhard Hoffmann
> >
> > _______________________________________________
> > Bioconductor mailing list
> > Bioconductor at stat.math.ethz.ch
> > https://stat.ethz.ch/mailman/listinfo/bioconductor
> >
> 
> --
> Thomas Girke
> University of California
> Riverside, CA 92521