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Galina, The IDs in these remapped CDFs are UniGene IDs ... so if you parse out the numeric ID (the ID without _at and Mm.), you should be able to get that info via tools in the biomaRt package directly without going back to Affy IDs. Regards, Duane _________________________________________________ Duane C. Hassane, Ph.D. Center for Pediatric Biomedical Research University of Rochester Medical Center 601 Elmwood Avenue, Box 703 Rochester, New York 14642 -----Original Message----- From: bioconductor-bounces@stat.math.ethz.ch [mailto:bioconductor-bounces at stat.math.ethz.ch]On Behalf Of Glazko, Galina Sent: Thursday, February 08, 2007 9:15 AM To: bioconductor at stat.math.ethz.ch Subject: [BioC] Chromosomal positions: mapping from custom cdf file Dear list, I am trying to retrieve the information about probes Chromosomal positions (with chromosome numbers) I used to used for that annaffy package, something like library('annaffy') probeids<-row.names(dat) symbols <- aafSymbol(probeids, "mouse4302") anncols <- aaf.handler()[c(1:2, 5:7,9)] anntable <- aafTableAnn(probeids, "mouse4302", anncols) but now I have custom cdf file which I got from http://brainarray.mbni.med.umich.edu <http: brainarray.mbni.med.umich.edu=""/> So, instead of Affy ID's now I have another IDs which are not recognizable by annaffy of course. It might be obvious, the mapping back from these IDs to Affy's IDs, but I am lost and do not know how to map them back. Or, may be there is a simpler way just to get Chr Numbers and Positions using these new IDs directly, without intermediate step of converting them back to Affy's? Could someone explain this to me? IDs in my expression file now look like this - Mm.8321_at, ... Out of curiosity I googled couple of them but found nothing... Thank you for your help! Best regards Galina [[alternative HTML version deleted]] _______________________________________________ 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 Galina, Glazko, Galina wrote: > Dear list, > > > > I am trying to retrieve the information about probes Chromosomal > positions (with chromosome numbers) > > I used to used for that annaffy package, something like > > > > library('annaffy') > > probeids<-row.names(dat) > > symbols <- aafSymbol(probeids, "mouse4302") > > anncols <- aaf.handler()[c(1:2, 5:7,9)] > > anntable <- aafTableAnn(probeids, "mouse4302", anncols) > > > > but now I have custom cdf file which I got from > > > > http://brainarray.mbni.med.umich.edu > <http: brainarray.mbni.med.umich.edu=""/> > > > > So, instead of Affy ID's now I have another IDs which are not > recognizable by annaffy of course. > > > > It might be obvious, the mapping back from these IDs to Affy's IDs, but > I am lost and do not know how to map them back. You don't want to map back to Affy IDs. The usual mapping is _from_ Affy IDs to something like Entrez Gene, UniGene, RefSeq, etc. By using the MBNI cdf you have already mapped probes ==> genes, so you want to go from there. > > Or, may be there is a simpler way just to get Chr Numbers and Positions > using these new IDs directly, without intermediate step of converting > them back to Affy's? > > Could someone explain this to me? IDs in my expression file now look > like this - Mm.8321_at, ... Yes. These ar UniGene IDs, with an _at added on because that is what MBNI tend to do. If you had googled Mm.8321 the first hit would have taken you here: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=unigene&term=Mm.8321 Anyway, IMO, the best thing to do from here on out is to use biomaRt to annotate your IDs. There are two ways you can go with biomaRt; either use one of the wrapper functions that Steffen has created such as getGene(), which will do something very similar to what you are doing with annaffy: > mart <- useMart("ensembl", "mmusculus_gene_ensembl") Checking attributes and filters ... ok > getGene("Mm.8321", "unigene", mart=mart) ID symbol 1 Mm.8321 Cit description 1 citron [Source:MarkerSymbol;Acc:MGI:105313] chromosome band strand chromosome_start 1 5 FALSE 1 116106643 chromosome_end ensembl_gene_id 1 116269946 ENSMUSG00000029516 ensembl_transcript_id 1 ENSMUST00000102560 or you can use getBM() directly to get whatever annotation you might like. See the vignette for more information. If you are using annaffy to create HTML tables, then you can use biomaRt in conjunction with the annotate package to do something very similar. There is a vignette that shows how to do that as well. HTH, Jim > > Out of curiosity I googled couple of them but found nothing... > > > > Thank you for your help! > > Best regards > > Galina > > > > > [[alternative HTML version deleted]] > > _______________________________________________ > 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, M.S. Biostatistician Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC 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.