[BioC] Affymetrix exon arrays?

[Steven McKinney]

Hi Jesse and Seth,

I need to start processing Affy Mouse Exon 1.0 ST
data.  I'm interested in the annotated data package - 
did anything further get done about creating a data package
from Jesse's work?  If not, are results still available
from Jesse via FTP?

We'd like to assess fold changes between mouse types
at the exon and gene level.  I've parsed affy-related
vignettes and R/BioC email trails, and don't see much
discussion on techniques for mapping exon data to
the gene level in R (saw one email response from Johannes
Rainer, April 10 2006, on getting gene level data out of
Affy's ExACT software, but we'd like to start with CEL
data and do our own normalization etc). 

Our cluster is not operational yet, so I will start processing
4 or 5 CEL files on an Apple Mac PowerPC G5 with 4 processors
and 4GB RAM.  I'm installing the latest R2.4.0/BioC release
and will see whether exon data can be processed in this environment.
Not sure whether I need 64 bit R or whether BioC packages
are 64bit aware.

If any one has done such analyses, and could share ideas 
and/or R code examples, it would be very much appreciated.


Best regards 

Steven McKinney

Statistician
Molecular Oncology and Breast Cancer Program
British Columbia Cancer Research Centre

email: smckinney at bccrc.ca
tel: 604-675-8000 x7561

BCCRC
Molecular Oncology
675 West 10th Ave, Floor 4
Vancouver B.C. 
V5Z 1L3

Canada


 

 


-----Original Message-----
From: bioconductor-bounces at stat.math.ethz.ch
[mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of Seth Falcon
Sent: Thursday, July 27, 2006 1:38 PM
To: Jesse Salisbury
Cc: bioconductor at stat.math.ethz.ch
Subject: Re: [BioC] Affymetrix exon arrays?

Hi Jesse,

Jesse Salisbury <ltboots at geneserver.mine.nu> writes:
> Hi All;      
> I have been working on the same problem, and have finally found a
computer    
> large enough to run it. Its a beowulf node at Jackson Labs with 16GB
of  
> memory. As it turns out, you need somwhere betwen 12.5 and 14GB for
the R 
> makecdfenv() package to process the MoEx-1_0-st-v1.cdf into a useable
R 
> environment. The process takes about 5hrs to complete on an  
> Opteron processor.      
>       
> I would like to make the files available, but I'm not sure how to post

> environments on bioconductor yet.      

We (Bioconductor) would be interested in hosting contributed
annotation data packages.  Right now the group here in Seattle is
fairly busy preparing for the BioC2006 conference (next week!).  If
you'd like to contribute the data package let us know (use the email
listed in the instructions for contributing a BioC package).

It sounds like you might just have an environment object and not a
package.  Creating a data package from that isn't too hard, but it
will require looking over the Writing R Extensions Manual...

+ seth

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