AffyProbes and genome

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David Kipling ▴ 110

@david-kipling-1252

Last seen 9.6 years ago

Hi The file Jim pointed you towards has a general location of the probeset (i.e. the region in which the 16 or thereabout probes are based). Somewhat more detail can be found in another Affymetrix file: http://www.affymetrix.com/Auth/analysis/downloads/psl/HG_U95Av2.link.p sl.zip This now gives a bp position (in the very last column) for each of the 16 probes in each probeset, rather than a single overall figure. Note that some probeset contain probes that map to different chrs, and thus there are multiple lines for some probesets. This figure for each probe may be enough for you; I believe (someone please correct me here!) that they are all 25mers, and if so then a single figure will enable you to work out the beginning and end of each probe. I have no idea whether the figure given is the start, middle, or 13th basepair, but this is something you could check quite quickly. However...if you want a very nice overview of the mapping of individual probes within a probeset to genomic and cDNA sequence information can I make a plug here for ADAPT, from Crispin's lab? Their paper is just out in Bioinformatics, and the site is: http://bioinf.picr.man.ac.uk/adapt/Welcome.adapt This may help you. Regards David Professor David Kipling Department of Pathology, School of Medicine, Cardiff University, Heath Park Cardiff CF14 4XN Email: KiplingD@cardiff.ac.uk Tel: +44 29 2074 4847 fax: +44 29 2074 4276 >>> Hrishikesh Deshmukh <d_hrishikesh@yahoo.com> 05/23/05 4:13 PM >>> Thank you very much sir, just one more question. The annotation file gives the "region" for each probeset_Id but is it possible to get the start and stop cooridnates for each of the 16 probes of a probeset_id. For ex. ProbeSet_ID| x|y| probeIndex| StartChrLoc| StopCHRLOC 1000_at 1 2 1 42545499 42545524 . .. ... 1001_at......................... I wonder where can i find this information. Thankyou very much again. Hrishi --- "James W. MacDonald" <jmacdon@med.umich.edu> wrote: > Hrishikesh Deshmukh wrote: > > Pardon my ignorance. > > How would i get the chromosomal locations written > to a > > text file for all the probes on HGU_95Av2. > > If all you want is the chromosomal locations in a > text file, I would > simply download the annotation file from Affy, and > delete all the other > columns. > > http://www.affymetrix.com/Auth/analysis/downloads/taf/HG_U95Av2_annot_ csv.zip > > This information is in the Genome Alignment column > of the file. > > Best, > > Jim > > > > > -- > James W. MacDonald > Affymetrix and cDNA Microarray Core > University of Michigan Cancer Center > 1500 E. Medical Center Drive > 7410 CCGC > Ann Arbor MI 48109 > 734-647-5623 > _______________________________________________ Bioconductor mailing list Bioconductor@stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/bioconductor

Microarray Alignment Annotation Cancer probe affy Microarray Alignment Annotation Cancer • 999 views

ADD COMMENT • link updated 18.9 years ago by Michael Janis ▴ 20 • written 18.9 years ago by David Kipling ▴ 110

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Michael Janis ▴ 20

@michael-janis-864

Last seen 9.6 years ago

Hello, I have a question about using vignettes as instructional material. I am a bioinformatics graduate student at UCLA and lead a summer seminar series on practical bioinformatics (tools and implementations). This summer I am preparing a course reader in the form of an O'Reilly Safari U. book (https://www.safariu.com/) - mainly a concatenation of various texts, published by O'Reilly, that satisfy the needs of this summer seminar series. I'd like very much to have permission to include several vignettes from the bioconductor website in this material - the material, although in the form of a "book" from O'Reilly printed sources, will remain private and only accessible to enrolled students for this seminar series at UCLA. Furthermore, all authors for all works within this reader will be cited, as would be bioconductor and vignette authors, with an addendum specifying that current version information can be found on the bioconductor website. I copy below, from the bioconductor website, the policy for using bioconductor vignettes for instructional purposes. I write today to ask, given the private nature of this course reader material, if I may include bioconductor vignettes in the final printed form. I would gladly accept any conditions you may request. In past offerings of this seminar series, I have found the vignettes to hold significant teaching value. Indeed, the vignettes were my own portal to effective use of bioconductor. I would very much like to offer enrolled students a comprehensive set of materials for this summer's seminar offering. Thank you for your consideration, Michael Janis Ph.D. Student, Bioinformatics, UCLA Using the vignettes: You are welcome to use these materials for instructional purposes. However, you may not include these in separately published works (articles, books, websites).When using all or parts of the Bioconductor course materials (slides, vignettes, scripts) we would appreciate it if you would cite the authors and refer your audience to the Bioconductor website

ADD COMMENT • link 18.9 years ago Michael Janis ▴ 20

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Hi Michael, Thanks for asking about this. Let me preface this by "I am not a lawyer", and if it is legal advice you are seeking then you should contact a professional. My understanding is that you need to decide which vignettes you would like and approach the copyright holders individualy. The project as a whole has no rights to grant you, individual packages are owned by their authors (or much more likely by their authors employers) and they would be in a position to say yes or no. Best wishes, Robert Michael Janis wrote: > Hello, > > I have a question about using vignettes as instructional material. I am a > bioinformatics graduate student at UCLA and lead a summer seminar series on > practical bioinformatics (tools and implementations). This summer I am > preparing a course reader in the form of an O'Reilly Safari U. book > (https://www.safariu.com/) - mainly a concatenation of various texts, > published by O'Reilly, that satisfy the needs of this summer seminar series. > I'd like very much to have permission to include several vignettes from the > bioconductor website in this material - the material, although in the form > of a "book" from O'Reilly printed sources, will remain private and only > accessible to enrolled students for this seminar series at UCLA. > Furthermore, all authors for all works within this reader will be cited, as > would be bioconductor and vignette authors, with an addendum specifying that > current version information can be found on the bioconductor website. > > I copy below, from the bioconductor website, the policy for using > bioconductor vignettes for instructional purposes. I write today to ask, > given the private nature of this course reader material, if I may include > bioconductor vignettes in the final printed form. I would gladly accept any > conditions you may request. In past offerings of this seminar series, I > have found the vignettes to hold significant teaching value. Indeed, the > vignettes were my own portal to effective use of bioconductor. I would very > much like to offer enrolled students a comprehensive set of materials for > this summer's seminar offering. > > Thank you for your consideration, > > Michael Janis > Ph.D. Student, Bioinformatics, UCLA > > > > Using the vignettes: You are welcome to use these materials for > instructional purposes. However, you may not include these in separately > published works (articles, books, websites).When using all or parts of the > Bioconductor course materials (slides, vignettes, scripts) we would > appreciate it if you would cite the authors and refer your audience to the > Bioconductor website > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor >

ADD REPLY • link 18.9 years ago rgentleman ★ 5.5k

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