[BiO BB] Affymetrix Data
Rohan Woodley
rgwoodley at sprynet.com
Thu Jan 30 21:24:31 EST 2003
A.Craig,
If I am understanding your questions correctly, I think you would need
the Chip Library file and the data file.
If that is the case, I have written a program the does the cross
referencing that can be modified to suit your needs.
For my particular need, I did not look for perfect match intensities,
however I am sure the program can be extended to take it
into consideration.
Let me know
Rohan.
a.craig wrote:
>Dear List,
>
>Does anyone know of any publicly available code for extracting individual
>perfect match and mismatch intensities for each probe pair of an affymetrix
>chip.
>
>Best wishes,
>
>Andrew Craig
>
>-----Original Message-----
>From: bio_bulletin_board-request at bioinformatics.org
>[mailto:bio_bulletin_board-request at bioinformatics.org]
>Sent: Thursday, January 30, 2003 5:01 PM
>To: bio_bulletin_board at bioinformatics.org
>Subject: BiO_Bulletin_Board digest, Vol 1 #395 - 1 msg
>
>
>Send BiO_Bulletin_Board mailing list submissions to
> bio_bulletin_board at bioinformatics.org
>
>To subscribe or unsubscribe via the World Wide Web, visit
> https://bioinformatics.org/mailman/listinfo/bio_bulletin_board
>or, via email, send a message with subject or body 'help' to
> bio_bulletin_board-request at bioinformatics.org
>
>You can reach the person managing the list at
> bio_bulletin_board-admin at bioinformatics.org
>
>When replying, please edit your Subject line so it is more specific
>than "Re: Contents of BiO_Bulletin_Board digest..."
>
>
>Today's Topics:
>
> 1. ACM PPDP'03 Call for Papers (Frank D. Valencia)
>
>--__--__--
>
>Message: 1
>Date: Thu, 30 Jan 2003 14:17:49 +0100
>From: "Frank D. Valencia" <frankv at it.uu.se>
>To: Corrado Priami <priami at dit.unitn.it>
>Cc: mt at sfc.keio.ac.jp, luca at microsoft.com, miyano at ims.u-tokyo.ac.jp,
> lincoln at csl.sri.com, gdp at dcs.ed.ac.uk, ina.koch at molgen.mpg.de,
> mh at informatik.tu-cottbus.de, olaf.wolkenhauer at umist.ac.uk,
> Finn.Drablos at sintef.no, mroux at pasteur.fr, priami at science.unitn.it,
> degano at di.unipi.it, baldari at unisi.it, ladbury at biochem.ucl.ac.uk,
> aviv at wisdom.weizmann.ac.il, valencia at cnb.uam.es,
> vschachter at hybrigenics.fr, lin at informatik.uni-rostock.de,
> Charles.Auffray at vjf.cnrs.fr, Alexander.Bockmayr at loria.fr,
> simon.plyte at pharmacia.com, Francois.Fages at inria.fr,
> danos at logique.jussieu.fr, edu at apbionet.org, abi at apbionet.org,
> abnet at angis.org.au, board at open-bio.org, i3c-pathways at www.i3c.org,
> necluster-l at necluster.org, moby-l at biomoby.org,
> bio_bulletin_board at bioinformatics.org,
> biodevelopers at bioinformatics.org, bioclusters at bioinformatics.org,
> announcements at vanbug.org, bioinf at vei.co.uk,
> bioinformatics at cs.uchicago.edu, announce at apbionet.org,
> discuss at apbionet.org, tchu at andrew.cmu.edu, gfc at cbmi.upmc.edu,
> cg09+ at andrew.cmu.edu, ddanks at ai.uwf.edu, dhandley at andrew.cmu.edu,
> mani at cbmi.upmc.edu, ODohertyR at msx.dept-med.pitt.edu, dgp+ at pitt.edu,
> jdramsey at andrew.cmu.edu, rsaavedra at ai.uwf.edu,
> rscheines at andrew.cmu.edu, nserban at andrew.cmu.edu, rbas at cs.cmu.edu,
> ps7z at andrew.cmu.edu, larry at stat.cmu.edu, wimberly3 at earthlink.net,
> cwyoo at cbmi.upmc.edu, jc12b at nih.gov, lauderdk at nigms.nih.gov,
> dg13w at nih.gov, pm4o at nih.gov, postowe at csr.nih.gov,
>katzf at mail.nih.gov,
> m8p at nih.gov, mm539c at nih.gov, ellenliberman at nih.gov,
> goodp at mail.nih.gov, brooksl at exchange.nih.gov, twerym at nhlbi.nih.gov,
> df18s at nih.gov, me25t at nih.gov, rm69e at nih.gov, ck82j at nih.gov,
> swajar at nibib.nih.gov, sourwine at nibib.nih.gov, fhaseltine at aol.com,
> ks79x at nih.gov, Barry_Davis at nih.gov, ek17w at nih.gov,
> hydej at extra.niddk.nih.gov, ws22e at nih.gov, mh38f at nih.gov,
> y15o at nih.gov, hs38k at nih.gov, mc105x at nih.gov, ivaisman at gmu.edu,
> cjamison at gmu.edu, sjafri at gmu.edu, Jan.Verwer at cwi.nl,
> lilia.alberghina at unimib.it, dan at biomed.bm.technion.ac.il,
> hw at bio.vu.nl, brazma at ebi.ac.uk, Bo.Servenius at astrazeneca.com,
> inge at ii.uib.no, bpn at mbb.ki.se, johnson at abo.fi, tmargus at ebc.ee,
> nikob at cbs.dtu.dk, ukkonen at cs.helsinki.fi, vissing at exiqon.com,
> daniel at decode.is, peleg at smi.stanford.edu, yeh at smi.stanford.edu,
> apo at gbf.de, acl2 at cs.utexas.edu, H.Schmidt at DKFZ-Heidelberg.de,
> agents at cs.umbc.edu, aiia at di.unito.it, alg at comm.toronto.edu,
> amast at cs.utwente.nl, announce at tcos.org, andrea.massa at ing.unitn.it,
> alessandro.bogliolo at uniurb.it, announcements.chi at acm.com,
> appiar at ncc.up.pt, atp at logic.tuwien.ac.at, asci at twi.tudelft.nl,
> bra-types at cs.chalmers.se, categories at mta.ca, ccl at dfki.uni-sb.de,
> clp at iscs.nus.edu.sg, cofi-reactive at brics.dk, comm-theory at ieee.org,
> concurrency at cwi.nl, conf at colmar.uha.fr,
> confs-conferencesa at comsoc.org, coq at margaux.inria,
> coq-club at pauillac.inria.fr, cs-logic at cs.indiana.edu,
> csl at dbai.tuwien.ac.at, csp at carlit.toulouse.inra.fr,
> dataloger at cs.chalmers.se, eacsl at dimi.uniud.it,
> frdist-obj at distributedcoalition.org, eapls-request at mailbase.ac.uk,
> eatcs-it-l at unifi.it, eatcs-it at cs.unibo.it, ecoop-info at ecoop.org,
> facs at lboro.ac.uk, eapls at jiscmail.ac.uk, ercim at cnuce.cnr.it,
> behavior at cs.ucsd.edu, formal-methods at cs.uidaho.edu,
> fsdm at it.uq.edu.au, ifip-tc6 at informatik.rwth-aachen.de,
> info-confs at comsoc.org, a_kapela at heart.med.upatras.gr,
> hise-safety-critical at minster.cs.york.ac.uk, ifmsig at cs.tcd.ie,
> info-hol at ultimate.cs.byu.edu, isabelle-users at cl.cam.ac.uk,
> jml at cs.iastate.edu, lambda-usergroup at dcs.ed.ac.uk,
> lfcs-interest at dcs.ed.ac.uk, itc at comsoc.org,
>logic at theory.lcs.mit.edu,
> news-announce-conferences at uunet.uu.net, softverf at nist.gov,
> lics at research.bell-labs.com, logic-announce at uclink4.berkeley.edu,
> logic-ml at logic.jaist.ac.jp, logic at cs.cornell.edu,
> lotos-world at sanson.dit.upm.es, nqthm-users at cli.com,
> nuprllist at cs.cornell.edu, nvti-list at cwi.nl, nwpt-info at sool.ioc.ee,
> om-announce at lars.math.fsu.edu, papm at dcs.ed.ac.uk,
> performance at haven.epm.ornl.gov, PetriNets at daimi.aau.dk,
> prog-lang at daimi.aau.dk, prog-lang at diku.dk, pvs at csl.sri.com,
> qed at mcs.anl.gov, reliable_computing at interval.usl.edu,
> rewriting at ens-lyon.fr, seworld at cs.colorado.edu,
> stochver at cs.bham.ac.uk, system-safety at listserv.gsfc.nasa.gov,
> theorem-provers at ai.mit.edu, theory-a at vm1.nodak.edu,
> theorynt at listserv.nodak.edu, vdm-forum at jiscmail.ac.uk,
> zeves at ora.on.ca, zforum at prg.ox.ac.uk, Bart.Jacobs at cs.kun.nl,
> comp-all at comp.lancs.ac.uk, traverso at itc.it, luca.degioia at unimib.it,
> milanesi at itba.mi.cnr.it, paolo at dsi.unifi.it, furlan at itc.it,
> laura.bonati at unimib.it, webmaster at systemsbiology.org,
> Lchalif at bioinformatics.weizmann.ac.il, Info at isb-sib.ch,
> Roslin.Bioinformatics at bbsrc.ac.uk, robin_deacle at ncbiotech.org,
> cubic at maple.bioc.columbia.edu, staff at sbc.su.se,
> drg at brc.dcs.gla.ac.uk, support at ebi.ac.uk,
>admin at mail.cryst.bbk.ac.uk,
> Queries at bioinf.man.ac.uk, director at bioinfo.ernet.in,
> winhide at sanbi.ac.za, info at sanbi.ac.za, brutlag at stanford.edu,
> kanehisa at kuicr.kyoto-u.ac.jp, goto at kuicr.kyoto-u.ac.jp,
> nakaya at kuicr.kyoto-u.ac.jp, shuichi at kuicr.kyoto-u.ac.jp,
> kaede at kuicr.kyoto-u.ac.jp, yuko at scl.kyoto-u.ac.jp,
> chiaki at scl.kyoto-u.ac.jp, asako at scl.kyoto-u.ac.jp,
> okuno at kuicr.kyoto-u.ac.jp, adeline at kuicr.kyoto-u.ac.jp,
> hirakawa at kuicr.kyoto-u.ac.jp, park at kuicr.kyoto-u.ac.jp,
> hattori at kuicr.kyoto-u.ac.jp, igarashi at kuicr.kyoto-u.ac.jp,
> katayama at kuicr.kyoto-u.ac.jp, acyshzw at kuicr.kyoto-u.ac.jp,
> kot at kuicr.kyoto-u.ac.jp, minowa at kuicr.kyoto-u.ac.jp,
> itoh at kuicr.kyoto-u.ac.jp, hizukuri at kuicr.kyoto-u.ac.jp,
> yoshi at kuicr.kyoto-u.ac.jp, takuji at kuicr.kyoto-u.ac.jp,
> okuda at kuicr.kyoto-u.ac.jp, rikuhiro at kuicr.kyoto-u.ac.jp,
> moriya at kuicr.kyoto-u.ac.jp, fujita at kuicr.kyoto-u.ac.jp,
> sato at kuicr.kyoto-u.ac.jp, naobumi at kuicr.kyoto-u.ac.jp,
> mtanaka at kuicr.kyoto-u.ac.jp, nati at kuicr.kyoto-u.ac.jp,
> toshi at scl.kyoto-u.ac.jp, tomomi at scl.kyoto-u.ac.jp,
> sanae at scl.kyoto-u.ac.jp, kayo at scl.kyoto-u.ac.jp,
> tomoko at scl.kyoto-u.ac.jp, nobue at scl.kyoto-u.ac.jp,
> megumi at scl.kyoto-u.ac.jp, rumiko at scl.kyoto-u.ac.jp,
> atsuko at scl.kyoto-u.ac.jp, junko at scl.kyoto-u.ac.jp,
> yuriko at scl.kyoto-u.ac.jp, yumi at scl.kyoto-u.ac.jp,
> njunko at scl.kyoto-u.ac.jp, miho at scl.kyoto-u.ac.jp,
> ktomoko at scl.kyoto-u.ac.jp, kana at scl.kyoto-u.ac.jp,
> fukumoto at scl.kyoto-u.ac.jp, kanae at scl.kyoto-u.ac.jp,
> kshirais at scl.kyoto-u.ac.jp, nishikaw at scl.kyoto-u.ac.jp,
> ohkubo at scl.kyoto-u.ac.jp, uehara at scl.kyoto-u.ac.jp,
> tonomura at scl.kyoto-u.ac.jp, furuta at scl.kyoto-u.ac.jp,
> konya at scl.kyoto-u.ac.jp, yamazaki at scl.kyoto-u.ac.jp,
> bioinformatics at ireland.com, rserra at oramont.it, axa at cs.purdue.edu,
> casadio at kaiser.alma.unibo.it, Heiko.Mueller at eu.pnu.com,
> Valencia at cnb.vam.es, Farisel at kaiser.alma.unibo.it,
> gigi at lipid.biocomp.unibo.it, soda at dsi.unifi.it, vullo at dsi.unifi.it,
> alex at mcculloch.ing.unifi.it, h-wilson at tamu.edu, jherreo at cnio.es,
> aadil_raiyan at usa.net, ponarul at usa.net,
>rajnishgupta73 at radiffmail.com,
> ewi at gbf.de, abi at gbf.de, kse at gbf.de, hom at gbf.de, ili at gbf.de,
> tcr at gbf.de, mch at gbf.de, ksl at gbf.de, vdr at gbf.de, dtj at cs.ucl.ac.uk,
> lmiller at cs.iastate.edu, lhb at iastate.edu, xgai at iastate.edu,
> melon at iq.usp.br, info at bioinformatics.buffalo.edu, info at ki.se,
> sdavids at uwc.ac.za, steipe at lmb.uni-muenchen.de,
> twclark at cs.uchicago.edu, ncox at genetics.bsd.uchicago.edu,
> s-endy at uchicago.edu, efrank at hep.uchicago.edu,
> dhl at genetics.bsd.uchicago.edu, rquigg at medicine.bsd.uchicago.edu,
> ridg at cs.uchicago.edu
>Subject: [BiO BB] ACM PPDP'03 Call for Papers
>Reply-To: bio_bulletin_board at bioinformatics.org
>
>
>Dear all,
>
>Apologies for multiple copies of this message. Please circulate the
>following call for papers to colleagues.
>
>Best wishes,
> Frank D. Valencia.
>
>-------------------
> Call for Papers
> Fifth ACM-SIGPLAN International Conference on
> Principles and Practice of Declarative Programming
> Uppsala, Sweden, 27-29 August 2003
>
>IMPORTANT DATES
> Submission 29 March 2003
> Notification 12 May 2003
> Final Version 13 June 2003
>
>WEB SITES
> PPDP 2003: http://www.it.uu.se/ppdp03/
> PLI 2003: http://www.it.uu.se/pli03/
> PPDP: http://pauillac.inria.fr/~fages/PPDP/.
>
>TOPICS (Not exhaustive): Logic and Constraint Programming; Functional
> Programming; Object-Oriented Programming; Concurrent Extensions;
> Mobile Computing; Integration of Paradigms; Proof Theoretic and
> Semantic Foundations; Program Design and Development; Type and Module
> Systems; Program Analysis and Verification; Program Transformation;
> Abstract Machines and Compilation; Programming Environments; and
> Application of Declarative Programming.
>
>CONFERENCE CHAIR: Konstantinos Sagonas, Uppsala University
> http://www.csd.uu.se/~kostis, email: kostis at it.uu.se
>
>PROGRAM CHAIR: Dale Miller, INRIA/Futurs & Ecole polytechnique
> http://www.lix.polytechnique.fr/Labo/Dale.Miller,
> email: Dale.Miller at inria.fr
>
>PROGRAM COMMITTEE
> Maria Alpuente, Univ. Politecnica de Valencia, ES
> Alessandra Di Pierro, Univ. of Pisa, IT
> Masami Hagiya, Univ. of Tokyo, JP
> Fergus Henderson, Univ. of Melbourne, AU
> Alberto Momigliano, Univ. of Leicester, UK
> Benjamin Pierce, Univ. of Pennsylvania, US
> C.R. Ramakrishnan, SUNY Stony Brook, US
> Mario Rodriguez Artalejo, Univ. Complutense, ES
> Amr Sabry, Univ. of Indiana, US
> Konstantinos Sagonas, Uppsala University, SW
> Frank Valencia, Uppsala University, SW
>
>PREVIOUS PPDP CONFERENCES
> Paris (1999), Montreal (2000), Firenze (2001), Pittsburgh (2002).
>
>SCOPE OF THE CONFERENCE: PPDP 2003 aims to stimulate research in the
>use of logical formalisms and methods for analyzing, specifying, and
>performing computations. Of general interest are all aspects
>surrounding declarative programming paradigms such as logic
>programming, functional logic programming, and constraint programming.
>Topics of more specific interest are enhancements to such formalisms
>with mechanisms for concurrency, mobility, modularity,
>object-orientation, and static analysis, as well as the fuller
>exploitation of the programming-as-proof-search framework through new
>designs and improved implementation methods. At the level of
>methodology, the use of logic based principles in the design of tools
>for program development, analysis, and verification relative to all
>programming paradigms is of interest. Papers related to the use of
>declarative paradigms and tools in industry and education are
>especially solicited. This list is not exhaustive: submissions
>related to new and interesting ideas relating broadly to declarative
>programming are encouraged. Prospective authors are welcome to
>communicate with the Program Chair about the suitability of a specific
>topic.
>
>PAPER SUBMISSIONS: Submissions must be made on or before 29 March
>2003, noon Central European Time and must be no more than 12 pages
>(including bibliography and appendices) and in standard ACM conference
>format: detailed formatting guidelines are available at
>http://www.acm.org/sigs/pubs/proceed/template.html, along with
>formatting templates or style files for LaTeX, Word Perfect, and Word.
>Proceedings will be published by ACM Press. Authors of accepted
>papers will be required to sign the ACM copyright form. Submissions
>will be carried out electronically via the Web via a link found at the
>conference web page. Papers must be submitted in either PDF format or
>as PostScript documents that are interpretable by Ghostscript. Papers
>must describe original, previously unpublished work that has not been
>simultaneously submitted for publication elsewhere. They must be
>written in English, must have a cover page with an abstract of up to
>200 words, keywords, postal and electronic mailing addresses, and
>phone and fax numbers of the corresponding author. Authors who wish
>to provide additional material to the reviewers beyond the 12-page
>limit can do so in clearly marked appendices: reviewers are not
>required to read such appendices. Submissions that do not meet these
>guidelines may not be considered.
>
>CONFERENCE VENUE AND RELATED EVENTS: PPDP 2003 is part of a federation
>meeting known as Principles, Logics and Implementations of high-level
>programming languages (PLI 2003) which includes the ACM SIGPLAN
>International Conference on Functional Programming (ICFP 2003). PLI
>will run from 25 - 29 August 2003. The meetings will take place on
>the Uppsala University campus.
>
>AFFILIATED WORKSHOPS: Proposals are solicited for PLI 2003 affiliated
>workshops. Details about the submission of proposals are available
>from the PLI 2003 web site. The deadline for workshop proposals is 14
>February 2003.
>
>STUDENT ATTENDEES: Students who have a paper accepted for the
>conference are offered student membership in SIGPLAN free for one
>year. As members of SIGPLAN they may apply for travel fellowships
>from the PAC fund.
>
>
>
>
>
>
More information about the BBB
mailing list