Search
Question: metadata - annotation package changes
0
gravatar for MARIA STALTERI
13.3 years ago by
MARIA STALTERI160 wrote:
Hi, I guess my question is mainly directed to John Zhang and the other authors/maintainers of the annotation packages for Affymetrix chips. In the latest versions (1.8) of the moe430a and rae230a packages, the probe set ID-to-accession number mappings (ACCNUM) are different from those given in previous versions (1.5, 1.6, 1.7). Can someone please explain to me why there has been a change? Regards, Maria.
ADD COMMENTlink modified 13.3 years ago by John Zhang2.9k • written 13.3 years ago by MARIA STALTERI160
0
gravatar for John Zhang
13.3 years ago by
John Zhang2.9k
John Zhang2.9k wrote:
Although I was involved in building 1.8, Seth is probably the best one to answer this question. My understanding is that, correct me Seth if I am wrong, a set of fresh base files (probe id to GeneBank accession number mappings extracted from Affymetrix) were used to build the new version of annotation packages. >X-Original-To: jzhang at jimmy.harvard.edu >Delivered-To: jzhang at jimmy.harvard.edu >Date: Tue, 9 Aug 2005 10:22:47 +0100 (BST) >From: Maria Stalteri <m.stalteri at="" mail.cryst.bbk.ac.uk=""> >X-X-Sender: hstal01 at sark.cryst.bbk.ac.uk >To: bioconductor at stat.math.ethz.ch >MIME-Version: 1.0 >X-cryst-bbk-ac-uk-MailScanner-Information: Please contact CCSG more information (http://www.cryst.bbk.ac.uk/CCSG/) >X-cryst-bbk-ac-uk-MailScanner: Found to be clean >X-cryst-bbk-ac-uk-MailScanner-SpamCheck: not spam, SpamAssassin (score=-3.906, required 9, BAYES_00 -4.90, FROM_ENDS_IN_NUMS 0.99) >X-Virus-Scanned: by amavisd-new at stat.math.ethz.ch >Subject: [BioC] metadata - annotation package changes >X-BeenThere: bioconductor at stat.math.ethz.ch >X-Mailman-Version: 2.1.6 >List-Id: The Bioconductor Project Mailing List <bioconductor.stat.math.ethz.ch> >List-Unsubscribe: <https: stat.ethz.ch="" mailman="" listinfo="" bioconductor="">, <mailto:bioconductor-request at="" stat.math.ethz.ch?subject="unsubscribe"> >List-Archive: <https: stat.ethz.ch="" pipermail="" bioconductor=""> >List-Post: <mailto:bioconductor at="" stat.math.ethz.ch=""> >List-Help: <mailto:bioconductor-request at="" stat.math.ethz.ch?subject="help"> >List-Subscribe: <https: stat.ethz.ch="" mailman="" listinfo="" bioconductor="">, <mailto:bioconductor-request at="" stat.math.ethz.ch?subject="subscribe"> >Content-Transfer-Encoding: 7bit >X-Spam-Checker-Version: SpamAssassin 3.0.1 (2004-10-22) on pascal.dfci.harvard.edu >X-Spam-Level: >X-Spam-Status: No, score=-2.6 required=3.0 tests=BAYES_00 autolearn=ham version=3.0.1 > >Hi, >I guess my question is mainly directed to John Zhang and >the other authors/maintainers of the annotation packages >for Affymetrix chips. > >In the latest versions (1.8) of the moe430a and rae230a >packages, the probe set ID-to-accession number mappings >(ACCNUM) are different from those given in previous >versions (1.5, 1.6, 1.7). > >Can someone please explain to me why there has been >a change? > >Regards, >Maria. > >_______________________________________________ >Bioconductor mailing list >Bioconductor at stat.math.ethz.ch >https://stat.ethz.ch/mailman/listinfo/bioconductor Jianhua Zhang Department of Medical Oncology Dana-Farber Cancer Institute 44 Binney Street Boston, MA 02115-6084
ADD COMMENTlink written 13.3 years ago by John Zhang2.9k
Hi John, If you were involved with building the previous releases you can probably tell me where the accession numbers for the previous releases (1.5,1.6,1.7) came from. Do you actually get them from the Affymetrix annotation files, and if so, which section? For some probe sets different sections of the Affymetrix files give different accession numbers. Many thanks, Maria. On Tue, 9 Aug 2005, John Zhang wrote: > Date: Tue, 9 Aug 2005 08:19:01 -0400 (EDT) > From: John Zhang <jzhang at="" jimmy.harvard.edu=""> > To: bioconductor at stat.math.ethz.ch, m.stalteri at mail.cryst.bbk.ac.uk > Subject: Re: [BioC] metadata - annotation package changes > > Although I was involved in building 1.8, Seth is probably the best one to answer > this question. My understanding is that, correct me Seth if I am wrong, a set of > fresh base files (probe id to GeneBank accession number mappings extracted from > Affymetrix) were used to build the new version of annotation packages. > > > > >X-Original-To: jzhang at jimmy.harvard.edu > >Delivered-To: jzhang at jimmy.harvard.edu > >Date: Tue, 9 Aug 2005 10:22:47 +0100 (BST) > >From: Maria Stalteri <m.stalteri at="" mail.cryst.bbk.ac.uk=""> > >X-X-Sender: hstal01 at sark.cryst.bbk.ac.uk > >To: bioconductor at stat.math.ethz.ch > >MIME-Version: 1.0 > >X-cryst-bbk-ac-uk-MailScanner-Information: Please contact CCSG more information > (http://www.cryst.bbk.ac.uk/CCSG/) > >X-cryst-bbk-ac-uk-MailScanner: Found to be clean > >X-cryst-bbk-ac-uk-MailScanner-SpamCheck: not spam, SpamAssassin (score=-3.906, > required 9, BAYES_00 -4.90, FROM_ENDS_IN_NUMS 0.99) > >X-Virus-Scanned: by amavisd-new at stat.math.ethz.ch > >Subject: [BioC] metadata - annotation package changes > >X-BeenThere: bioconductor at stat.math.ethz.ch > >X-Mailman-Version: 2.1.6 > >List-Id: The Bioconductor Project Mailing List <bioconductor.stat.math.ethz.ch> > >List-Unsubscribe: <https: stat.ethz.ch="" mailman="" listinfo="" bioconductor="">, > <mailto:bioconductor-request at="" stat.math.ethz.ch?subject="unsubscribe"> > >List-Archive: <https: stat.ethz.ch="" pipermail="" bioconductor=""> > >List-Post: <mailto:bioconductor at="" stat.math.ethz.ch=""> > >List-Help: <mailto:bioconductor-request at="" stat.math.ethz.ch?subject="help"> > >List-Subscribe: <https: stat.ethz.ch="" mailman="" listinfo="" bioconductor="">, > <mailto:bioconductor-request at="" stat.math.ethz.ch?subject="subscribe"> > >Content-Transfer-Encoding: 7bit > >X-Spam-Checker-Version: SpamAssassin 3.0.1 (2004-10-22) on > pascal.dfci.harvard.edu > >X-Spam-Level: > >X-Spam-Status: No, score=-2.6 required=3.0 tests=BAYES_00 autolearn=ham > version=3.0.1 > > > >Hi, > >I guess my question is mainly directed to John Zhang and > >the other authors/maintainers of the annotation packages > >for Affymetrix chips. > > > >In the latest versions (1.8) of the moe430a and rae230a > >packages, the probe set ID-to-accession number mappings > >(ACCNUM) are different from those given in previous > >versions (1.5, 1.6, 1.7). > > > >Can someone please explain to me why there has been > >a change? > > > >Regards, > >Maria. > > > >_______________________________________________ > >Bioconductor mailing list > >Bioconductor at stat.math.ethz.ch > >https://stat.ethz.ch/mailman/listinfo/bioconductor > > Jianhua Zhang > Department of Medical Oncology > Dana-Farber Cancer Institute > 44 Binney Street > Boston, MA 02115-6084 >
ADD REPLYlink written 13.3 years ago by MARIA STALTERI160
0
gravatar for John Zhang
13.3 years ago by
John Zhang2.9k
John Zhang2.9k wrote:
http://www.affymetrix.com/support/technical/byproduct.affx? >If you were involved with building the previous releases you can probably >tell me where the >accession numbers for the previous releases (1.5,1.6,1.7) >came from. >Do you actually get them from the Affymetrix annotation files, >and if so, which section? For some probe sets different sections >of the Affymetrix files give different accession numbers. CSV files for chips under http://www.affymetrix.com/support/technical/byproduct.affx? > >Many thanks, >Maria. > > >On Tue, 9 Aug 2005, John Zhang wrote: > >> Date: Tue, 9 Aug 2005 08:19:01 -0400 (EDT) >> From: John Zhang <jzhang at="" jimmy.harvard.edu=""> >> To: bioconductor at stat.math.ethz.ch, m.stalteri at mail.cryst.bbk.ac.uk >> Subject: Re: [BioC] metadata - annotation package changes >> >> Although I was involved in building 1.8, Seth is probably the best one to answer >> this question. My understanding is that, correct me Seth if I am wrong, a set of >> fresh base files (probe id to GeneBank accession number mappings extracted from >> Affymetrix) were used to build the new version of annotation packages. >> >> >> >> >X-Original-To: jzhang at jimmy.harvard.edu >> >Delivered-To: jzhang at jimmy.harvard.edu >> >Date: Tue, 9 Aug 2005 10:22:47 +0100 (BST) >> >From: Maria Stalteri <m.stalteri at="" mail.cryst.bbk.ac.uk=""> >> >X-X-Sender: hstal01 at sark.cryst.bbk.ac.uk >> >To: bioconductor at stat.math.ethz.ch >> >MIME-Version: 1.0 >> >X-cryst-bbk-ac-uk-MailScanner-Information: Please contact CCSG more information >> (http://www.cryst.bbk.ac.uk/CCSG/) >> >X-cryst-bbk-ac-uk-MailScanner: Found to be clean >> >X-cryst-bbk-ac-uk-MailScanner-SpamCheck: not spam, SpamAssassin (score=-3.906, >> required 9, BAYES_00 -4.90, FROM_ENDS_IN_NUMS 0.99) >> >X-Virus-Scanned: by amavisd-new at stat.math.ethz.ch >> >Subject: [BioC] metadata - annotation package changes >> >X-BeenThere: bioconductor at stat.math.ethz.ch >> >X-Mailman-Version: 2.1.6 >> >List-Id: The Bioconductor Project Mailing List <bioconductor.stat.math.ethz.ch> >> >List-Unsubscribe: <https: stat.ethz.ch="" mailman="" listinfo="" bioconductor="">, >> <mailto:bioconductor-request at="" stat.math.ethz.ch?subject="unsubscribe"> >> >List-Archive: <https: stat.ethz.ch="" pipermail="" bioconductor=""> >> >List-Post: <mailto:bioconductor at="" stat.math.ethz.ch=""> >> >List-Help: <mailto:bioconductor-request at="" stat.math.ethz.ch?subject="help"> >> >List-Subscribe: <https: stat.ethz.ch="" mailman="" listinfo="" bioconductor="">, >> <mailto:bioconductor-request at="" stat.math.ethz.ch?subject="subscribe"> >> >Content-Transfer-Encoding: 7bit >> >X-Spam-Checker-Version: SpamAssassin 3.0.1 (2004-10-22) on >> pascal.dfci.harvard.edu >> >X-Spam-Level: >> >X-Spam-Status: No, score=-2.6 required=3.0 tests=BAYES_00 autolearn=ham >> version=3.0.1 >> > >> >Hi, >> >I guess my question is mainly directed to John Zhang and >> >the other authors/maintainers of the annotation packages >> >for Affymetrix chips. >> > >> >In the latest versions (1.8) of the moe430a and rae230a >> >packages, the probe set ID-to-accession number mappings >> >(ACCNUM) are different from those given in previous >> >versions (1.5, 1.6, 1.7). >> > >> >Can someone please explain to me why there has been >> >a change? >> > >> >Regards, >> >Maria. >> > >> >_______________________________________________ >> >Bioconductor mailing list >> >Bioconductor at stat.math.ethz.ch >> >https://stat.ethz.ch/mailman/listinfo/bioconductor >> >> Jianhua Zhang >> Department of Medical Oncology >> Dana-Farber Cancer Institute >> 44 Binney Street >> Boston, MA 02115-6084 >> Jianhua Zhang Department of Medical Oncology Dana-Farber Cancer Institute 44 Binney Street Boston, MA 02115-6084
ADD COMMENTlink written 13.3 years ago by John Zhang2.9k
Previously I have been using R Version 2.0.1 on a Linux box as root and everything worked well. I have installed in my local user director the latest R Version 2.1.1 on a different machine (a Sun box) from the source code and I am not running as root. I can't quite figure out how to make getBioC() not constantly rebuild/reinstall the entire Bioconductor Affy suite every time. I do the "source ("http://www.bioconductor.org/getBioC.R") and "getBioc("affy") and it always re-gets it; unlike on the Linux box as root where it just said " all requested packages are up to date". I have fiddled with the lib argument to getBioC() and I have set the R_HOME and R_LIB environment variables. There may be an subtle incantation I need but can't quite figure out. Anybody got any ideas? How do you force the darn thing to recognize that it has built the thing before?
ADD REPLYlink written 13.3 years ago by Richard Finney180
OK, but what release of the Affymetrix csv files was used for the previous annotation packages, and which field of the csv files did the accession numbers come from? Thanks for trying to answer my question. Maria. On Tue, 9 Aug 2005, John Zhang wrote: > Date: Tue, 9 Aug 2005 09:45:42 -0400 (EDT) > From: John Zhang <jzhang at="" jimmy.harvard.edu=""> > To: jzhang at jimmy.harvard.edu, m.stalteri at mail.cryst.bbk.ac.uk > Cc: bioconductor at stat.math.ethz.ch, m.stalteri at mail.cryst.bbk.ac.uk > Subject: Re: [BioC] metadata - annotation package changes > > http://www.affymetrix.com/support/technical/byproduct.affx? > > >If you were involved with building the previous releases you can probably > >tell me where the > >accession numbers for the previous releases (1.5,1.6,1.7) > >came from. > >Do you actually get them from the Affymetrix annotation files, > >and if so, which section? For some probe sets different sections > >of the Affymetrix files give different accession numbers. > > CSV files for chips under > http://www.affymetrix.com/support/technical/byproduct.affx? > > > > > >Many thanks, > >Maria. > > > > > >On Tue, 9 Aug 2005, John Zhang wrote: > > > >> Date: Tue, 9 Aug 2005 08:19:01 -0400 (EDT) > >> From: John Zhang <jzhang at="" jimmy.harvard.edu=""> > >> To: bioconductor at stat.math.ethz.ch, m.stalteri at mail.cryst.bbk.ac.uk > >> Subject: Re: [BioC] metadata - annotation package changes > >> > >> Although I was involved in building 1.8, Seth is probably the best one to > answer > >> this question. My understanding is that, correct me Seth if I am wrong, a set > of > >> fresh base files (probe id to GeneBank accession number mappings extracted > from > >> Affymetrix) were used to build the new version of annotation packages. > >> > >> > >> > >> >X-Original-To: jzhang at jimmy.harvard.edu > >> >Delivered-To: jzhang at jimmy.harvard.edu > >> >Date: Tue, 9 Aug 2005 10:22:47 +0100 (BST) > >> >From: Maria Stalteri <m.stalteri at="" mail.cryst.bbk.ac.uk=""> > >> >X-X-Sender: hstal01 at sark.cryst.bbk.ac.uk > >> >To: bioconductor at stat.math.ethz.ch > >> >MIME-Version: 1.0 > >> >X-cryst-bbk-ac-uk-MailScanner-Information: Please contact CCSG more > information > >> (http://www.cryst.bbk.ac.uk/CCSG/) > >> >X-cryst-bbk-ac-uk-MailScanner: Found to be clean > >> >X-cryst-bbk-ac-uk-MailScanner-SpamCheck: not spam, SpamAssassin > (score=-3.906, > >> required 9, BAYES_00 -4.90, FROM_ENDS_IN_NUMS 0.99) > >> >X-Virus-Scanned: by amavisd-new at stat.math.ethz.ch > >> >Subject: [BioC] metadata - annotation package changes > >> >X-BeenThere: bioconductor at stat.math.ethz.ch > >> >X-Mailman-Version: 2.1.6 > >> >List-Id: The Bioconductor Project Mailing List > <bioconductor.stat.math.ethz.ch> > >> >List-Unsubscribe: <https: stat.ethz.ch="" mailman="" listinfo="" bioconductor="">, > >> <mailto:bioconductor-request at="" stat.math.ethz.ch?subject="unsubscribe"> > >> >List-Archive: <https: stat.ethz.ch="" pipermail="" bioconductor=""> > >> >List-Post: <mailto:bioconductor at="" stat.math.ethz.ch=""> > >> >List-Help: <mailto:bioconductor-request at="" stat.math.ethz.ch?subject="help"> > >> >List-Subscribe: <https: stat.ethz.ch="" mailman="" listinfo="" bioconductor="">, > >> <mailto:bioconductor-request at="" stat.math.ethz.ch?subject="subscribe"> > >> >Content-Transfer-Encoding: 7bit > >> >X-Spam-Checker-Version: SpamAssassin 3.0.1 (2004-10-22) on > >> pascal.dfci.harvard.edu > >> >X-Spam-Level: > >> >X-Spam-Status: No, score=-2.6 required=3.0 tests=BAYES_00 autolearn=ham > >> version=3.0.1 > >> > > >> >Hi, > >> >I guess my question is mainly directed to John Zhang and > >> >the other authors/maintainers of the annotation packages > >> >for Affymetrix chips. > >> > > >> >In the latest versions (1.8) of the moe430a and rae230a > >> >packages, the probe set ID-to-accession number mappings > >> >(ACCNUM) are different from those given in previous > >> >versions (1.5, 1.6, 1.7). > >> > > >> >Can someone please explain to me why there has been > >> >a change? > >> > > >> >Regards, > >> >Maria. > >> > > >> >_______________________________________________ > >> >Bioconductor mailing list > >> >Bioconductor at stat.math.ethz.ch > >> >https://stat.ethz.ch/mailman/listinfo/bioconductor > >> > >> Jianhua Zhang > >> Department of Medical Oncology > >> Dana-Farber Cancer Institute > >> 44 Binney Street > >> Boston, MA 02115-6084 > >> > > Jianhua Zhang > Department of Medical Oncology > Dana-Farber Cancer Institute > 44 Binney Street > Boston, MA 02115-6084 >
ADD REPLYlink written 13.3 years ago by MARIA STALTERI160
0
gravatar for John Zhang
13.3 years ago by
John Zhang2.9k
John Zhang2.9k wrote:
>OK, but what release of the Affymetrix csv files >was used for the previous annotation packages, >and which field of the csv files did the accession numbers come from? We did not keep the information back then as it was a little hard to extract the dates for the files programmatically from Affymetrix web site. Should be on the to do list. The field for accession numbers is "Representative Public ID" > >Thanks for trying to answer my question. >Maria. > > >On Tue, 9 Aug 2005, John Zhang wrote: > >> Date: Tue, 9 Aug 2005 09:45:42 -0400 (EDT) >> From: John Zhang <jzhang at="" jimmy.harvard.edu=""> >> To: jzhang at jimmy.harvard.edu, m.stalteri at mail.cryst.bbk.ac.uk >> Cc: bioconductor at stat.math.ethz.ch, m.stalteri at mail.cryst.bbk.ac.uk >> Subject: Re: [BioC] metadata - annotation package changes >> >> http://www.affymetrix.com/support/technical/byproduct.affx? >> >> >If you were involved with building the previous releases you can probably >> >tell me where the >> >accession numbers for the previous releases (1.5,1.6,1.7) >> >came from. >> >Do you actually get them from the Affymetrix annotation files, >> >and if so, which section? For some probe sets different sections >> >of the Affymetrix files give different accession numbers. >> >> CSV files for chips under >> http://www.affymetrix.com/support/technical/byproduct.affx? >> >> >> > >> >Many thanks, >> >Maria. >> > >> > >> >On Tue, 9 Aug 2005, John Zhang wrote: >> > >> >> Date: Tue, 9 Aug 2005 08:19:01 -0400 (EDT) >> >> From: John Zhang <jzhang at="" jimmy.harvard.edu=""> >> >> To: bioconductor at stat.math.ethz.ch, m.stalteri at mail.cryst.bbk.ac.uk >> >> Subject: Re: [BioC] metadata - annotation package changes >> >> >> >> Although I was involved in building 1.8, Seth is probably the best one to >> answer >> >> this question. My understanding is that, correct me Seth if I am wrong, a set >> of >> >> fresh base files (probe id to GeneBank accession number mappings extracted >> from >> >> Affymetrix) were used to build the new version of annotation packages. >> >> >> >> >> >> >> >> >X-Original-To: jzhang at jimmy.harvard.edu >> >> >Delivered-To: jzhang at jimmy.harvard.edu >> >> >Date: Tue, 9 Aug 2005 10:22:47 +0100 (BST) >> >> >From: Maria Stalteri <m.stalteri at="" mail.cryst.bbk.ac.uk=""> >> >> >X-X-Sender: hstal01 at sark.cryst.bbk.ac.uk >> >> >To: bioconductor at stat.math.ethz.ch >> >> >MIME-Version: 1.0 >> >> >X-cryst-bbk-ac-uk-MailScanner-Information: Please contact CCSG more >> information >> >> (http://www.cryst.bbk.ac.uk/CCSG/) >> >> >X-cryst-bbk-ac-uk-MailScanner: Found to be clean >> >> >X-cryst-bbk-ac-uk-MailScanner-SpamCheck: not spam, SpamAssassin >> (score=-3.906, >> >> required 9, BAYES_00 -4.90, FROM_ENDS_IN_NUMS 0.99) >> >> >X-Virus-Scanned: by amavisd-new at stat.math.ethz.ch >> >> >Subject: [BioC] metadata - annotation package changes >> >> >X-BeenThere: bioconductor at stat.math.ethz.ch >> >> >X-Mailman-Version: 2.1.6 >> >> >List-Id: The Bioconductor Project Mailing List >> <bioconductor.stat.math.ethz.ch> >> >> >List-Unsubscribe: <https: stat.ethz.ch="" mailman="" listinfo="" bioconductor="">, >> >> <mailto:bioconductor-request at="" stat.math.ethz.ch?subject="unsubscribe"> >> >> >List-Archive: <https: stat.ethz.ch="" pipermail="" bioconductor=""> >> >> >List-Post: <mailto:bioconductor at="" stat.math.ethz.ch=""> >> >> >List-Help: <mailto:bioconductor-request at="" stat.math.ethz.ch?subject="help"> >> >> >List-Subscribe: <https: stat.ethz.ch="" mailman="" listinfo="" bioconductor="">, >> >> <mailto:bioconductor-request at="" stat.math.ethz.ch?subject="subscribe"> >> >> >Content-Transfer-Encoding: 7bit >> >> >X-Spam-Checker-Version: SpamAssassin 3.0.1 (2004-10-22) on >> >> pascal.dfci.harvard.edu >> >> >X-Spam-Level: >> >> >X-Spam-Status: No, score=-2.6 required=3.0 tests=BAYES_00 autolearn=ham >> >> version=3.0.1 >> >> > >> >> >Hi, >> >> >I guess my question is mainly directed to John Zhang and >> >> >the other authors/maintainers of the annotation packages >> >> >for Affymetrix chips. >> >> > >> >> >In the latest versions (1.8) of the moe430a and rae230a >> >> >packages, the probe set ID-to-accession number mappings >> >> >(ACCNUM) are different from those given in previous >> >> >versions (1.5, 1.6, 1.7). >> >> > >> >> >Can someone please explain to me why there has been >> >> >a change? >> >> > >> >> >Regards, >> >> >Maria. >> >> > >> >> >_______________________________________________ >> >> >Bioconductor mailing list >> >> >Bioconductor at stat.math.ethz.ch >> >> >https://stat.ethz.ch/mailman/listinfo/bioconductor >> >> >> >> Jianhua Zhang >> >> Department of Medical Oncology >> >> Dana-Farber Cancer Institute >> >> 44 Binney Street >> >> Boston, MA 02115-6084 >> >> >> >> Jianhua Zhang >> Department of Medical Oncology >> Dana-Farber Cancer Institute >> 44 Binney Street >> Boston, MA 02115-6084 >> > >_______________________________________________ >Bioconductor mailing list >Bioconductor at stat.math.ethz.ch >https://stat.ethz.ch/mailman/listinfo/bioconductor Jianhua Zhang Department of Medical Oncology Dana-Farber Cancer Institute 44 Binney Street Boston, MA 02115-6084
ADD COMMENTlink written 13.3 years ago by John Zhang2.9k
Can you remember roughly when the previous time that you extracted the accession numbers from the Affymetrix files was? I keep asking because as far as I can tell, the Affymetrix Representative Public IDs have not changed since the first version of the annotation files that I have worked with, which was June 2004 (but I know that the first release of the Affy files was March 2003). I have asked Affymetrix whether the Representative Public IDs were static data or not, but I didn't get a very precise reply. Many thanks, Maria. On Wed, 10 Aug 2005, John Zhang wrote: > Date: Wed, 10 Aug 2005 08:17:13 -0400 (EDT) > From: John Zhang <jzhang at="" jimmy.harvard.edu=""> > To: jzhang at jimmy.harvard.edu, m.stalteri at mail.cryst.bbk.ac.uk > Cc: m.stalteri at mail.cryst.bbk.ac.uk, bioconductor at stat.math.ethz.ch > Subject: Re: [BioC] metadata - annotation package changes > > > >OK, but what release of the Affymetrix csv files > >was used for the previous annotation packages, > >and which field of the csv files did the accession numbers come from? > > We did not keep the information back then as it was a little hard to extract the > dates for the files programmatically from Affymetrix web site. Should be on the > to do list. > > The field for accession numbers is "Representative Public ID" > > > > > >Thanks for trying to answer my question. > >Maria. > > > > > >On Tue, 9 Aug 2005, John Zhang wrote: > > > >> Date: Tue, 9 Aug 2005 09:45:42 -0400 (EDT) > >> From: John Zhang <jzhang at="" jimmy.harvard.edu=""> > >> To: jzhang at jimmy.harvard.edu, m.stalteri at mail.cryst.bbk.ac.uk > >> Cc: bioconductor at stat.math.ethz.ch, m.stalteri at mail.cryst.bbk.ac.uk > >> Subject: Re: [BioC] metadata - annotation package changes > >> > >> http://www.affymetrix.com/support/technical/byproduct.affx? > >> > >> >If you were involved with building the previous releases you can probably > >> >tell me where the > >> >accession numbers for the previous releases (1.5,1.6,1.7) > >> >came from. > >> >Do you actually get them from the Affymetrix annotation files, > >> >and if so, which section? For some probe sets different sections > >> >of the Affymetrix files give different accession numbers. > >> > >> CSV files for chips under > >> http://www.affymetrix.com/support/technical/byproduct.affx? > >> > >> > >> > > >> >Many thanks, > >> >Maria. > >> > > >> > > >> >On Tue, 9 Aug 2005, John Zhang wrote: > >> > > >> >> Date: Tue, 9 Aug 2005 08:19:01 -0400 (EDT) > >> >> From: John Zhang <jzhang at="" jimmy.harvard.edu=""> > >> >> To: bioconductor at stat.math.ethz.ch, m.stalteri at mail.cryst.bbk.ac.uk > >> >> Subject: Re: [BioC] metadata - annotation package changes > >> >> > >> >> Although I was involved in building 1.8, Seth is probably the best one to > >> answer > >> >> this question. My understanding is that, correct me Seth if I am wrong, a > set > >> of > >> >> fresh base files (probe id to GeneBank accession number mappings extracted > >> from > >> >> Affymetrix) were used to build the new version of annotation packages. > >> >> > >> >> > >> >> > >> >> >X-Original-To: jzhang at jimmy.harvard.edu > >> >> >Delivered-To: jzhang at jimmy.harvard.edu > >> >> >Date: Tue, 9 Aug 2005 10:22:47 +0100 (BST) > >> >> >From: Maria Stalteri <m.stalteri at="" mail.cryst.bbk.ac.uk=""> > >> >> >X-X-Sender: hstal01 at sark.cryst.bbk.ac.uk > >> >> >To: bioconductor at stat.math.ethz.ch > >> >> >MIME-Version: 1.0 > >> >> >X-cryst-bbk-ac-uk-MailScanner-Information: Please contact CCSG more > >> information > >> >> (http://www.cryst.bbk.ac.uk/CCSG/) > >> >> >X-cryst-bbk-ac-uk-MailScanner: Found to be clean > >> >> >X-cryst-bbk-ac-uk-MailScanner-SpamCheck: not spam, SpamAssassin > >> (score=-3.906, > >> >> required 9, BAYES_00 -4.90, FROM_ENDS_IN_NUMS 0.99) > >> >> >X-Virus-Scanned: by amavisd-new at stat.math.ethz.ch > >> >> >Subject: [BioC] metadata - annotation package changes > >> >> >X-BeenThere: bioconductor at stat.math.ethz.ch > >> >> >X-Mailman-Version: 2.1.6 > >> >> >List-Id: The Bioconductor Project Mailing List > >> <bioconductor.stat.math.ethz.ch> > >> >> >List-Unsubscribe: <https: stat.ethz.ch="" mailman="" listinfo="" bioconductor="">, > >> >> <mailto:bioconductor-request at="" stat.math.ethz.ch?subject="unsubscribe"> > >> >> >List-Archive: <https: stat.ethz.ch="" pipermail="" bioconductor=""> > >> >> >List-Post: <mailto:bioconductor at="" stat.math.ethz.ch=""> > >> >> >List-Help: <mailto:bioconductor-request at="" stat.math.ethz.ch?subject="help"> > >> >> >List-Subscribe: <https: stat.ethz.ch="" mailman="" listinfo="" bioconductor="">, > >> >> <mailto:bioconductor-request at="" stat.math.ethz.ch?subject="subscribe"> > >> >> >Content-Transfer-Encoding: 7bit > >> >> >X-Spam-Checker-Version: SpamAssassin 3.0.1 (2004-10-22) on > >> >> pascal.dfci.harvard.edu > >> >> >X-Spam-Level: > >> >> >X-Spam-Status: No, score=-2.6 required=3.0 tests=BAYES_00 autolearn=ham > >> >> version=3.0.1 > >> >> > > >> >> >Hi, > >> >> >I guess my question is mainly directed to John Zhang and > >> >> >the other authors/maintainers of the annotation packages > >> >> >for Affymetrix chips. > >> >> > > >> >> >In the latest versions (1.8) of the moe430a and rae230a > >> >> >packages, the probe set ID-to-accession number mappings > >> >> >(ACCNUM) are different from those given in previous > >> >> >versions (1.5, 1.6, 1.7). > >> >> > > >> >> >Can someone please explain to me why there has been > >> >> >a change? > >> >> > > >> >> >Regards, > >> >> >Maria. > >> >> > > >> >> >_______________________________________________ > >> >> >Bioconductor mailing list > >> >> >Bioconductor at stat.math.ethz.ch > >> >> >https://stat.ethz.ch/mailman/listinfo/bioconductor > >> >> > >> >> Jianhua Zhang > >> >> Department of Medical Oncology > >> >> Dana-Farber Cancer Institute > >> >> 44 Binney Street > >> >> Boston, MA 02115-6084 > >> >> > >> > >> Jianhua Zhang > >> Department of Medical Oncology > >> Dana-Farber Cancer Institute > >> 44 Binney Street > >> Boston, MA 02115-6084 > >> > > > >_______________________________________________ > >Bioconductor mailing list > >Bioconductor at stat.math.ethz.ch > >https://stat.ethz.ch/mailman/listinfo/bioconductor > > Jianhua Zhang > Department of Medical Oncology > Dana-Farber Cancer Institute > 44 Binney Street > Boston, MA 02115-6084 >
ADD REPLYlink written 13.3 years ago by MARIA STALTERI160
0
gravatar for John Zhang
13.3 years ago by
John Zhang2.9k
John Zhang2.9k wrote:
>Can you remember roughly when the previous time that you >extracted the accession numbers from the Affymetrix files was? I believe it was before June 2004. Check the date of build for 1.5. > > >I keep asking because as far as I can tell, the Affymetrix >Representative Public IDs have not changed since the first version >of the annotation files that I have worked with, which was >June 2004 (but I know that the first release of the Affy files was March >2003). >I have asked Affymetrix whether the Representative Public IDs >were static data or not, but I didn't get a very precise reply. > >Many thanks, >Maria. > > >On Wed, 10 Aug 2005, John Zhang wrote: > >> Date: Wed, 10 Aug 2005 08:17:13 -0400 (EDT) >> From: John Zhang <jzhang at="" jimmy.harvard.edu=""> >> To: jzhang at jimmy.harvard.edu, m.stalteri at mail.cryst.bbk.ac.uk >> Cc: m.stalteri at mail.cryst.bbk.ac.uk, bioconductor at stat.math.ethz.ch >> Subject: Re: [BioC] metadata - annotation package changes >> >> >> >OK, but what release of the Affymetrix csv files >> >was used for the previous annotation packages, >> >and which field of the csv files did the accession numbers come from? >> >> We did not keep the information back then as it was a little hard to extract the >> dates for the files programmatically from Affymetrix web site. Should be on the >> to do list. >> >> The field for accession numbers is "Representative Public ID" >> >> >> > >> >Thanks for trying to answer my question. >> >Maria. >> > >> > >> >On Tue, 9 Aug 2005, John Zhang wrote: >> > >> >> Date: Tue, 9 Aug 2005 09:45:42 -0400 (EDT) >> >> From: John Zhang <jzhang at="" jimmy.harvard.edu=""> >> >> To: jzhang at jimmy.harvard.edu, m.stalteri at mail.cryst.bbk.ac.uk >> >> Cc: bioconductor at stat.math.ethz.ch, m.stalteri at mail.cryst.bbk.ac.uk >> >> Subject: Re: [BioC] metadata - annotation package changes >> >> >> >> http://www.affymetrix.com/support/technical/byproduct.affx? >> >> >> >> >If you were involved with building the previous releases you can probably >> >> >tell me where the >> >> >accession numbers for the previous releases (1.5,1.6,1.7) >> >> >came from. >> >> >Do you actually get them from the Affymetrix annotation files, >> >> >and if so, which section? For some probe sets different sections >> >> >of the Affymetrix files give different accession numbers. >> >> >> >> CSV files for chips under >> >> http://www.affymetrix.com/support/technical/byproduct.affx? >> >> >> >> >> >> > >> >> >Many thanks, >> >> >Maria. >> >> > >> >> > >> >> >On Tue, 9 Aug 2005, John Zhang wrote: >> >> > >> >> >> Date: Tue, 9 Aug 2005 08:19:01 -0400 (EDT) >> >> >> From: John Zhang <jzhang at="" jimmy.harvard.edu=""> >> >> >> To: bioconductor at stat.math.ethz.ch, m.stalteri at mail.cryst.bbk.ac.uk >> >> >> Subject: Re: [BioC] metadata - annotation package changes >> >> >> >> >> >> Although I was involved in building 1.8, Seth is probably the best one to >> >> answer >> >> >> this question. My understanding is that, correct me Seth if I am wrong, a >> set >> >> of >> >> >> fresh base files (probe id to GeneBank accession number mappings extracted >> >> from >> >> >> Affymetrix) were used to build the new version of annotation packages. >> >> >> >> >> >> >> >> >> >> >> >> >X-Original-To: jzhang at jimmy.harvard.edu >> >> >> >Delivered-To: jzhang at jimmy.harvard.edu >> >> >> >Date: Tue, 9 Aug 2005 10:22:47 +0100 (BST) >> >> >> >From: Maria Stalteri <m.stalteri at="" mail.cryst.bbk.ac.uk=""> >> >> >> >X-X-Sender: hstal01 at sark.cryst.bbk.ac.uk >> >> >> >To: bioconductor at stat.math.ethz.ch >> >> >> >MIME-Version: 1.0 >> >> >> >X-cryst-bbk-ac-uk-MailScanner-Information: Please contact CCSG more >> >> information >> >> >> (http://www.cryst.bbk.ac.uk/CCSG/) >> >> >> >X-cryst-bbk-ac-uk-MailScanner: Found to be clean >> >> >> >X-cryst-bbk-ac-uk-MailScanner-SpamCheck: not spam, SpamAssassin >> >> (score=-3.906, >> >> >> required 9, BAYES_00 -4.90, FROM_ENDS_IN_NUMS 0.99) >> >> >> >X-Virus-Scanned: by amavisd-new at stat.math.ethz.ch >> >> >> >Subject: [BioC] metadata - annotation package changes >> >> >> >X-BeenThere: bioconductor at stat.math.ethz.ch >> >> >> >X-Mailman-Version: 2.1.6 >> >> >> >List-Id: The Bioconductor Project Mailing List >> >> <bioconductor.stat.math.ethz.ch> >> >> >> >List-Unsubscribe: <https: stat.ethz.ch="" mailman="" listinfo="" bioconductor="">, >> >> >> <mailto:bioconductor-request at="" stat.math.ethz.ch?subject="unsubscribe"> >> >> >> >List-Archive: <https: stat.ethz.ch="" pipermail="" bioconductor=""> >> >> >> >List-Post: <mailto:bioconductor at="" stat.math.ethz.ch=""> >> >> >> >List-Help: <mailto:bioconductor-request at="" stat.math.ethz.ch?subject="help"> >> >> >> >List-Subscribe: <https: stat.ethz.ch="" mailman="" listinfo="" bioconductor="">, >> >> >> <mailto:bioconductor-request at="" stat.math.ethz.ch?subject="subscribe"> >> >> >> >Content-Transfer-Encoding: 7bit >> >> >> >X-Spam-Checker-Version: SpamAssassin 3.0.1 (2004-10-22) on >> >> >> pascal.dfci.harvard.edu >> >> >> >X-Spam-Level: >> >> >> >X-Spam-Status: No, score=-2.6 required=3.0 tests=BAYES_00 autolearn=ham >> >> >> version=3.0.1 >> >> >> > >> >> >> >Hi, >> >> >> >I guess my question is mainly directed to John Zhang and >> >> >> >the other authors/maintainers of the annotation packages >> >> >> >for Affymetrix chips. >> >> >> > >> >> >> >In the latest versions (1.8) of the moe430a and rae230a >> >> >> >packages, the probe set ID-to-accession number mappings >> >> >> >(ACCNUM) are different from those given in previous >> >> >> >versions (1.5, 1.6, 1.7). >> >> >> > >> >> >> >Can someone please explain to me why there has been >> >> >> >a change? >> >> >> > >> >> >> >Regards, >> >> >> >Maria. >> >> >> > >> >> >> >_______________________________________________ >> >> >> >Bioconductor mailing list >> >> >> >Bioconductor at stat.math.ethz.ch >> >> >> >https://stat.ethz.ch/mailman/listinfo/bioconductor >> >> >> >> >> >> Jianhua Zhang >> >> >> Department of Medical Oncology >> >> >> Dana-Farber Cancer Institute >> >> >> 44 Binney Street >> >> >> Boston, MA 02115-6084 >> >> >> >> >> >> >> Jianhua Zhang >> >> Department of Medical Oncology >> >> Dana-Farber Cancer Institute >> >> 44 Binney Street >> >> Boston, MA 02115-6084 >> >> >> > >> >_______________________________________________ >> >Bioconductor mailing list >> >Bioconductor at stat.math.ethz.ch >> >https://stat.ethz.ch/mailman/listinfo/bioconductor >> >> Jianhua Zhang >> Department of Medical Oncology >> Dana-Farber Cancer Institute >> 44 Binney Street >> Boston, MA 02115-6084 >> Jianhua Zhang Department of Medical Oncology Dana-Farber Cancer Institute 44 Binney Street Boston, MA 02115-6084
ADD COMMENTlink written 13.3 years ago by John Zhang2.9k
The 1.5 packages were built in March 2004. On Wed, 10 Aug 2005, John Zhang wrote: > Date: Wed, 10 Aug 2005 09:13:17 -0400 (EDT) > From: John Zhang <jzhang at="" jimmy.harvard.edu=""> > To: jzhang at jimmy.harvard.edu, m.stalteri at mail.cryst.bbk.ac.uk > Cc: m.stalteri at mail.cryst.bbk.ac.uk, bioconductor at stat.math.ethz.ch > Subject: Re: [BioC] metadata - annotation package changes > > > >Can you remember roughly when the previous time that you > >extracted the accession numbers from the Affymetrix files was? > > I believe it was before June 2004. Check the date of build for 1.5. > > > > > > >I keep asking because as far as I can tell, the Affymetrix > >Representative Public IDs have not changed since the first version > >of the annotation files that I have worked with, which was > >June 2004 (but I know that the first release of the Affy files was March > >2003). > >I have asked Affymetrix whether the Representative Public IDs > >were static data or not, but I didn't get a very precise reply. > > > >Many thanks, > >Maria. > > > > > >On Wed, 10 Aug 2005, John Zhang wrote: > > > >> Date: Wed, 10 Aug 2005 08:17:13 -0400 (EDT) > >> From: John Zhang <jzhang at="" jimmy.harvard.edu=""> > >> To: jzhang at jimmy.harvard.edu, m.stalteri at mail.cryst.bbk.ac.uk > >> Cc: m.stalteri at mail.cryst.bbk.ac.uk, bioconductor at stat.math.ethz.ch > >> Subject: Re: [BioC] metadata - annotation package changes > >> > >> > >> >OK, but what release of the Affymetrix csv files > >> >was used for the previous annotation packages, > >> >and which field of the csv files did the accession numbers come from? > >> > >> We did not keep the information back then as it was a little hard to extract > the > >> dates for the files programmatically from Affymetrix web site. Should be on > the > >> to do list. > >> > >> The field for accession numbers is "Representative Public ID" > >> > >> > >> > > >> >Thanks for trying to answer my question. > >> >Maria. > >> > > >> > > >> >On Tue, 9 Aug 2005, John Zhang wrote: > >> > > >> >> Date: Tue, 9 Aug 2005 09:45:42 -0400 (EDT) > >> >> From: John Zhang <jzhang at="" jimmy.harvard.edu=""> > >> >> To: jzhang at jimmy.harvard.edu, m.stalteri at mail.cryst.bbk.ac.uk > >> >> Cc: bioconductor at stat.math.ethz.ch, m.stalteri at mail.cryst.bbk.ac.uk > >> >> Subject: Re: [BioC] metadata - annotation package changes > >> >> > >> >> http://www.affymetrix.com/support/technical/byproduct.affx? > >> >> > >> >> >If you were involved with building the previous releases you can probably > >> >> >tell me where the > >> >> >accession numbers for the previous releases (1.5,1.6,1.7) > >> >> >came from. > >> >> >Do you actually get them from the Affymetrix annotation files, > >> >> >and if so, which section? For some probe sets different sections > >> >> >of the Affymetrix files give different accession numbers. > >> >> > >> >> CSV files for chips under > >> >> http://www.affymetrix.com/support/technical/byproduct.affx? > >> >> > >> >> > >> >> > > >> >> >Many thanks, > >> >> >Maria. > >> >> > > >> >> > > >> >> >On Tue, 9 Aug 2005, John Zhang wrote: > >> >> > > >> >> >> Date: Tue, 9 Aug 2005 08:19:01 -0400 (EDT) > >> >> >> From: John Zhang <jzhang at="" jimmy.harvard.edu=""> > >> >> >> To: bioconductor at stat.math.ethz.ch, m.stalteri at mail.cryst.bbk.ac.uk > >> >> >> Subject: Re: [BioC] metadata - annotation package changes > >> >> >> > >> >> >> Although I was involved in building 1.8, Seth is probably the best one > to > >> >> answer > >> >> >> this question. My understanding is that, correct me Seth if I am wrong, > a > >> set > >> >> of > >> >> >> fresh base files (probe id to GeneBank accession number mappings > extracted > >> >> from > >> >> >> Affymetrix) were used to build the new version of annotation packages. > >> >> >> > >> >> >> > >> >> >> > >> >> >> >X-Original-To: jzhang at jimmy.harvard.edu > >> >> >> >Delivered-To: jzhang at jimmy.harvard.edu > >> >> >> >Date: Tue, 9 Aug 2005 10:22:47 +0100 (BST) > >> >> >> >From: Maria Stalteri <m.stalteri at="" mail.cryst.bbk.ac.uk=""> > >> >> >> >X-X-Sender: hstal01 at sark.cryst.bbk.ac.uk > >> >> >> >To: bioconductor at stat.math.ethz.ch > >> >> >> >MIME-Version: 1.0 > >> >> >> >X-cryst-bbk-ac-uk-MailScanner-Information: Please contact CCSG more > >> >> information > >> >> >> (http://www.cryst.bbk.ac.uk/CCSG/) > >> >> >> >X-cryst-bbk-ac-uk-MailScanner: Found to be clean > >> >> >> >X-cryst-bbk-ac-uk-MailScanner-SpamCheck: not spam, SpamAssassin > >> >> (score=-3.906, > >> >> >> required 9, BAYES_00 -4.90, FROM_ENDS_IN_NUMS 0.99) > >> >> >> >X-Virus-Scanned: by amavisd-new at stat.math.ethz.ch > >> >> >> >Subject: [BioC] metadata - annotation package changes > >> >> >> >X-BeenThere: bioconductor at stat.math.ethz.ch > >> >> >> >X-Mailman-Version: 2.1.6 > >> >> >> >List-Id: The Bioconductor Project Mailing List > >> >> <bioconductor.stat.math.ethz.ch> > >> >> >> >List-Unsubscribe: > <https: stat.ethz.ch="" mailman="" listinfo="" bioconductor="">, > >> >> >> <mailto:bioconductor-request at="" stat.math.ethz.ch?subject="unsubscribe"> > >> >> >> >List-Archive: <https: stat.ethz.ch="" pipermail="" bioconductor=""> > >> >> >> >List-Post: <mailto:bioconductor at="" stat.math.ethz.ch=""> > >> >> >> >List-Help: > <mailto:bioconductor-request at="" stat.math.ethz.ch?subject="help"> > >> >> >> >List-Subscribe: <https: stat.ethz.ch="" mailman="" listinfo="" bioconductor="">, > >> >> >> <mailto:bioconductor-request at="" stat.math.ethz.ch?subject="subscribe"> > >> >> >> >Content-Transfer-Encoding: 7bit > >> >> >> >X-Spam-Checker-Version: SpamAssassin 3.0.1 (2004-10-22) on > >> >> >> pascal.dfci.harvard.edu > >> >> >> >X-Spam-Level: > >> >> >> >X-Spam-Status: No, score=-2.6 required=3.0 tests=BAYES_00 > autolearn=ham > >> >> >> version=3.0.1 > >> >> >> > > >> >> >> >Hi, > >> >> >> >I guess my question is mainly directed to John Zhang and > >> >> >> >the other authors/maintainers of the annotation packages > >> >> >> >for Affymetrix chips. > >> >> >> > > >> >> >> >In the latest versions (1.8) of the moe430a and rae230a > >> >> >> >packages, the probe set ID-to-accession number mappings > >> >> >> >(ACCNUM) are different from those given in previous > >> >> >> >versions (1.5, 1.6, 1.7). > >> >> >> > > >> >> >> >Can someone please explain to me why there has been > >> >> >> >a change? > >> >> >> > > >> >> >> >Regards, > >> >> >> >Maria. > >> >> >> > > >> >> >> >_______________________________________________ > >> >> >> >Bioconductor mailing list > >> >> >> >Bioconductor at stat.math.ethz.ch > >> >> >> >https://stat.ethz.ch/mailman/listinfo/bioconductor > >> >> >> > >> >> >> Jianhua Zhang > >> >> >> Department of Medical Oncology > >> >> >> Dana-Farber Cancer Institute > >> >> >> 44 Binney Street > >> >> >> Boston, MA 02115-6084 > >> >> >> > >> >> > >> >> Jianhua Zhang > >> >> Department of Medical Oncology > >> >> Dana-Farber Cancer Institute > >> >> 44 Binney Street > >> >> Boston, MA 02115-6084 > >> >> > >> > > >> >_______________________________________________ > >> >Bioconductor mailing list > >> >Bioconductor at stat.math.ethz.ch > >> >https://stat.ethz.ch/mailman/listinfo/bioconductor > >> > >> Jianhua Zhang > >> Department of Medical Oncology > >> Dana-Farber Cancer Institute > >> 44 Binney Street > >> Boston, MA 02115-6084 > >> > > Jianhua Zhang > Department of Medical Oncology > Dana-Farber Cancer Institute > 44 Binney Street > Boston, MA 02115-6084 >
ADD REPLYlink written 13.3 years ago by MARIA STALTERI160
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.2.0
Traffic: 439 users visited in the last hour