Hello, I would like to map some probes to their chromosome location. I am using the Affimetrix mu74a chip, so I have the Affimetrix call names like 100981_at, 93026_at, 101898_s_at, 97564_f_at, 98790_s_at, etc. now I would like to know in which chromosome they are and at which distance from the centromere. Is this possible with the bioconductor package? Thanks H.Ghezzo Meakins-Christie Labs Montreal - Canada

hi, you should take a look at the annotate() package. chromLoc-class Class chromLoc, a class for describing the location of a gene on a chromosome. chromLocation-class Class chromLocation, a class for describing genes and their chromosome mappings. I haven't dealt much with chromosome locations, I deal mainly with creating web pages based on genbank and locuslink ids, but these functions may be the first place to start. hth, richard park computational data analyzer joslin diabetes center -----Original Message----- From: R.Heberto Ghezzo [mailto:heberto.ghezzo@mcgill.ca] Sent: Wednesday, June 25, 2003 13:36 PM To: bioconductor@stat.math.ethz.ch Subject: [BioC] Re: location in chromosome Hello, I would like to map some probes to their chromosome location. I am using the Affimetrix mu74a chip, so I have the Affimetrix call names like 100981_at, 93026_at, 101898_s_at, 97564_f_at, 98790_s_at, etc. now I would like to know in which chromosome they are and at which distance from the centromere. Is this possible with the bioconductor package? Thanks H.Ghezzo Meakins-Christie Labs Montreal - Canada _______________________________________________ Bioconductor mailing list Bioconductor@stat.math.ethz.ch https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor

> Hello, > I would like to map some probes to their chromosome location. I am using > the Affimetrix mu74a chip, so I have the Affimetrix call names like > 100981_at, 93026_at, 101898_s_at, 97564_f_at, 98790_s_at, etc. > now I would like to know in which chromosome they are and at which > distance from the centromere. Previous replies to this emphasized the annotate/chromLocation structures that work for various organisms. If you work through the byChroms vignette in geneplotter substituting the mgu74av2 package for hu6800, you will get the resources that answer this question. at a lower level, it may be worth mentioning that package mgu74av2 has environments mgu74av2CHRLOC and mgu74av2CHR which map from the probeset names noted above (100981_at etc) to oriented nucleotide counts and chromosome numbers respectively all the chip-targeted metadata resources should have these *CHRLOC and *CHR environments that can be queried for this sort of information. > Is this possible with the bioconductor package? > Thanks > H.Ghezzo > Meakins-Christie Labs > Montreal - Canada > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor >