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@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 _______________________________________________ Bioconductor mailing list Bioconductor at stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor

Hi Steven; Here is a link to the exon array environment. ftp://geneserver.mine.nu/affy/moex10stv1cdf.affy.v2.tar.gz It is based on the affy exon probeset mappings. It can run on a machine with 4Gb of memory, but can easily use 8-12Gb depending on what your trying to do. There are other probeset environments available for this platform at Bioconductor (refseq, ensembl, etc.) which are much more memory friendly. I haven't seen much for alternative transcript structure packages at Bioconductor yet. I have been doing most of my analysis with mysql tables and perl scripts. They seem to handle the enormous dataset size better. Mysql works well with the multi-level probe->exon->transcript->gene mappings. Jesse **************************************************************** Jesse Salisbury Functional Genomics University of Maine email: jesse.salisbury at umit.maine.edu ph: 207-731-8318 web: http://geneserver.mine.nu/ ***************************************************************** On Thursday 05 October 2006 15:27, Steven McKinney wrote: > 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 --