hello, i'm a researcher at Boston U. and a user of Bioconductor. currently, Affymetrix-provided CDF library files associate each probe with a single probe set -- a one-to-one mapping -- even when that probe is known to cross-hybridize to other probe sets (or more precisely, when that probe cross-hybrizes to other regions of sequence targeted by other probe sets). an ideal CDF library file would have a one-to-many mapping of a probe to probe sets. in an actual CDF file, this would mean that a probe's x,y coordinates and description line would be listed in multiple unit blocks -- instead of just once. would such a file work with existing Bioconductor packages? does the current implementation require a single association of probe--> probe sets? i have looked through Laurent Gautier's altcdfenvs package but have not found whether such a re-mapping would be possible. any insights would be much appreciated. sincerely, mike ___________________ michael driscoll bioinformatics program boston university http://www.bu.edu/abl http://gardnerlab.bu.edu

hello, i'm a researcher at Boston U. and a user of Bioconductor. currently, Affymetrix-provided CDF library files associate each probe with a single probe set -- a one-to-one mapping -- even when that probe is known to cross-hybridize to other probe sets (or more precisely, when that probe cross-hybrizes to other regions of sequence targeted by other probe sets). an ideal CDF library file would have a one-to-many mapping of a probe to probe sets. in an actual CDF file, this would mean that a probe's description line would show up in multiple unit blocks -- instead of just once. would such a file work with existing Bioconductor packages? does the current implementation require a unique association of probe--> probe sets? i have looked through Laurent Gautier's altcdfenvs package but have not found whether such a re-mapping would be possible. any insights would be much appreciated. sincerely, mike ___________________ michael driscoll bioinformatics program boston university http://www.bu.edu/abl http://gardnerlab.bu.edu

Hi Michael, it should be straightforward to prepare a CDF environment as you describe from your own probe-transcriptome alignment, and afaIk most (or all) functions in the affy package etc would work. However, why would you want to do this? If anything, I'd have thought one wants to exclude probes that have multiple matches, rather than have them sit around in (and contaminate) multiple places. If a probe hits multiple places in the genome, this is in almost all cases not sporadic, but because the hit regions share a common ancestor. Best wishes Wolfgang > > i'm a researcher at Boston U. and a user of Bioconductor. > > currently, Affymetrix-provided CDF library files associate each probe > with a single probe set -- a one-to-one mapping -- even when that > probe is known to cross-hybridize to other probe sets (or more > precisely, when that probe cross-hybrizes to other regions of sequence > targeted by other probe sets). > > an ideal CDF library file would have a one-to-many mapping of a probe > to probe sets. in an actual CDF file, this would mean that a probe's > x,y coordinates and description line would be listed in multiple unit > blocks -- instead of just once. > > would such a file work with existing Bioconductor packages? does the > current implementation require a single association of probe--> probe > sets? > > i have looked through Laurent Gautier's altcdfenvs package but have > not found whether such a re-mapping would be possible. > > any insights would be much appreciated. > > sincerely, mike > ___________________ > michael driscoll > bioinformatics program > boston university > http://www.bu.edu/abl > http://gardnerlab.bu.edu > > _______________________________________________ > 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 -- Best regards Wolfgang ------------------------------------- Wolfgang Huber European Bioinformatics Institute European Molecular Biology Laboratory Cambridge CB10 1SD England Phone: +44 1223 494642 Fax: +44 1223 494486 Http: www.ebi.ac.uk/huber

michael driscoll wrote: > hello, > > i'm a researcher at Boston U. and a user of Bioconductor. > > currently, Affymetrix-provided CDF library files associate each probe > with a single probe set -- a one-to-one mapping -- even when that > probe is known to cross-hybridize to other probe sets (or more > precisely, when that probe cross-hybrizes to other regions of sequence > targeted by other probe sets). > > an ideal CDF library file would have a one-to-many mapping of a probe > to probe sets. in an actual CDF file, this would mean that a probe's > x,y coordinates and description line would be listed in multiple unit > blocks -- instead of just once. One might argue that an ideal cdf package would eliminate cross-hybridizing probes so you could be sure that you are only interrogating one transcript per probeset. We now have packages (cdf and probe) that do just that - supplied to us by the folks at the Molecular and Behavioral Neuroscience Institute at UMich. If you are interested, you can browse these packages using biocViews: http://www.bioconductor.org/packages/1.8/AnnotationData.html and more information can be found on the MBNI web page: http://brainarray.mhri.med.umich.edu/Brainarray/Database/CustomCDF/gen omic_curated_CDF.asp Best, Jim > > would such a file work with existing Bioconductor packages? does the > current implementation require a single association of probe--> probe > sets? > > i have looked through Laurent Gautier's altcdfenvs package but have > not found whether such a re-mapping would be possible. > > any insights would be much appreciated. > > sincerely, mike > ___________________ > michael driscoll > bioinformatics program > boston university > http://www.bu.edu/abl > http://gardnerlab.bu.edu > > _______________________________________________ > 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 -- James W. MacDonald University of Michigan Affymetrix and cDNA Microarray Core 1500 E Medical Center Drive Ann Arbor MI 48109 734-647-5623 ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues.

Whatever your reasons are for wanting a probe to concurrently appear in different probe sets, this is indeed not handled by the package altcdfenvs. The idea was to contruct whatever mapping directly in R (and skip the potentially painful procedure of creating CDF files, just to see them read into R right after). If you want to have probes appearing in several probe sets, I would wait for after pre-processing data (background correction, normalization). If you want to use your very own mapping (for reason that might belong to your particular experimental setting -e.g., using a slightly different species than the one the chip was designed against, or using using it with a transgenic organism-, or supplementary knowledge you might have), the package 'atltcdfenvs' will be your friend. Tasks like removing cross-hybridizing probes will be easy (in that case, a single call to the function "unique.CdfEnvAffy" will do the job). Laurent > hello, > > i'm a researcher at Boston U. and a user of Bioconductor. > > currently, Affymetrix-provided CDF library files associate each probe > with a single probe set -- a one-to-one mapping -- even when that > probe is known to cross-hybridize to other probe sets (or more > precisely, when that probe cross-hybrizes to other regions of sequence > targeted by other probe sets). > > an ideal CDF library file would have a one-to-many mapping of a probe > to probe sets. in an actual CDF file, this would mean that a probe's > x,y coordinates and description line would be listed in multiple unit > blocks -- instead of just once. > > would such a file work with existing Bioconductor packages? does the > current implementation require a single association of probe--> probe > sets? > > i have looked through Laurent Gautier's altcdfenvs package but have > not found whether such a re-mapping would be possible. > > any insights would be much appreciated. > > sincerely, mike > ___________________ > michael driscoll > bioinformatics program > boston university > http://www.bu.edu/abl > http://gardnerlab.bu.edu > > _______________________________________________ > 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 >