where to download 'probeset.cvs' file for creating scheme file
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Steve Shen ▴ 330
@steve-shen-3743
Last seen 9.6 years ago
Dear Christian, A quick question about creating scheme files, I am trying to download 'transcripts.cvs' and 'probeset.cvs' files from http://www.affymetrix.com/support/technical/annotationfilesmain.affx?h ightlight=true&rootCategoryId=. It seemed to be that only transcripts.cvs available from affy site. Can you or someone else point me out where to find the files? Thanks, Steve [[alternative HTML version deleted]]
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cstrato ★ 3.9k
@cstrato-908
Last seen 5.5 years ago
Austria
Dear Steve, For some reason Affymetrix has reorganized their web-site in a way so that it is really hard to find anything!! As far as I can see, go to: http://www.affymetrix.com/support/mas/index.affx then "Select a product" e.g. HuExon array, then check "Software & Data" i.e. "Annotation Files" and "Library Files" then click "Go". The resulting page contains "Current NetAffx Annotation Files" which contains both the transcript and probeset annotation files. Best regards Christian Steve Shen wrote: > Dear Christian, > > A quick question about creating scheme files, I am trying to download > 'transcripts.cvs' and 'probeset.cvs' files from > http://www.affymetrix.com/support/technical/annotationfilesmain.affx ?hightlight=true&rootCategoryId= > <http: www.affymetrix.com="" support="" technical="" annotationfilesmain.aff="" x?hightlight="true&amp;rootCategoryId=">. > It seemed to be that only transcripts.cvs available from affy site. > Can you or someone else point me out where to find the files? Thanks, > > Steve
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On 03/07/2010 11:59 AM, cstrato wrote: > Dear Steve, > > For some reason Affymetrix has reorganized their web-site in a way so > that it is really hard to find anything!! > > As far as I can see, go to: > http://www.affymetrix.com/support/mas/index.affx > then "Select a product" e.g. HuExon array, > then check "Software & Data" i.e. "Annotation Files" and "Library Files" > then click "Go". > The resulting page contains "Current NetAffx Annotation Files" which > contains both the transcript and probeset annotation files. Not that the following is guaranteed to be robust to affy file movement, but library(AffyCompatible) rsrc <- NetAffxResource("your at username", "password") names(rsrc) rsrc[["HuEx-1_0-st-v2"]] rsrc[["HuEx-1_0-st-v2"]][[1]]] sapply(affxAnnotation(rsrc[["HuEx-1_0-st-v2"]]), affxDescription) anno <- affxFile(rsrc[["HuEx-1_0-st-v2", "Probeset Annotations, CSV Format"]]) csv <- readAnnotation(rsrc, annotation=anno) The vignette "Annotation retrieval with NetAffxResource" is a useful starting place. Martin > > Best regards > Christian > > > Steve Shen wrote: >> Dear Christian, >> >> A quick question about creating scheme files, I am trying to download >> 'transcripts.cvs' and 'probeset.cvs' files from >> http://www.affymetrix.com/support/technical/annotationfilesmain.aff x?hightlight=true&rootCategoryId= >> <http: www.affymetrix.com="" support="" technical="" annotationfilesmain.af="" fx?hightlight="true&amp;rootCategoryId=">. >> It seemed to be that only transcripts.cvs available from affy site. >> Can you or someone else point me out where to find the files? Thanks, >> >> Steve > > _______________________________________________ > 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 -- Martin Morgan Computational Biology / Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: Arnold Building M1 B861 Phone: (206) 667-2793
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Dear Christian and Martin, Thanks so much for your help. I got what I wanted. However, will that be possible for xps users to have a scheme file repository? It might be two much work for your team. Thanks again, Steve On Sun, Mar 7, 2010 at 3:19 PM, Martin Morgan <mtmorgan@fhcrc.org> wrote: > On 03/07/2010 11:59 AM, cstrato wrote: > > Dear Steve, > > > > For some reason Affymetrix has reorganized their web-site in a way so > > that it is really hard to find anything!! > > > > As far as I can see, go to: > > http://www.affymetrix.com/support/mas/index.affx > > then "Select a product" e.g. HuExon array, > > then check "Software & Data" i.e. "Annotation Files" and "Library Files" > > then click "Go". > > The resulting page contains "Current NetAffx Annotation Files" which > > contains both the transcript and probeset annotation files. > > Not that the following is guaranteed to be robust to affy file movement, > but > > library(AffyCompatible) > rsrc <- NetAffxResource("your@username", "password") > names(rsrc) > rsrc[["HuEx-1_0-st-v2"]] > rsrc[["HuEx-1_0-st-v2"]][[1]]] > sapply(affxAnnotation(rsrc[["HuEx-1_0-st-v2"]]), affxDescription) > anno <- affxFile(rsrc[["HuEx-1_0-st-v2", > "Probeset Annotations, CSV Format"]]) > csv <- readAnnotation(rsrc, annotation=anno) > > The vignette "Annotation retrieval with NetAffxResource" is a useful > starting place. > > Martin > > > > > > > Best regards > > Christian > > > > > > Steve Shen wrote: > >> Dear Christian, > >> > >> A quick question about creating scheme files, I am trying to download > >> 'transcripts.cvs' and 'probeset.cvs' files from > >> > http://www.affymetrix.com/support/technical/annotationfilesmain.affx ?hightlight=true&rootCategoryId= > >> < > http://www.affymetrix.com/support/technical/annotationfilesmain.affx ?hightlight=true&rootCategoryId= > >. > >> It seemed to be that only transcripts.cvs available from affy site. > >> Can you or someone else point me out where to find the files? Thanks, > >> > >> Steve > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor@stat.math.ethz.ch > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > Search the archives: > > http://news.gmane.org/gmane.science.biology.informatics.conductor > > > -- > Martin Morgan > Computational Biology / Fred Hutchinson Cancer Research Center > 1100 Fairview Ave. N. > PO Box 19024 Seattle, WA 98109 > > Location: Arnold Building M1 B861 > Phone: (206) 667-2793 > [[alternative HTML version deleted]]
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Dear Steve, In principle I can create the scheme files for the mostly used arrays (since I do it anyhow for testing purposes), the only question is where to upload the scheme files. Best regards Christian Steve Shen wrote: > Dear Christian and Martin, > > Thanks so much for your help. I got what I wanted. However, will that > be possible for xps users to have a scheme file repository? It might > be two much work for your team. Thanks again, > > Steve > > On Sun, Mar 7, 2010 at 3:19 PM, Martin Morgan <mtmorgan at="" fhcrc.org=""> <mailto:mtmorgan at="" fhcrc.org="">> wrote: > > On 03/07/2010 11:59 AM, cstrato wrote: > > Dear Steve, > > > > For some reason Affymetrix has reorganized their web-site in a > way so > > that it is really hard to find anything!! > > > > As far as I can see, go to: > > http://www.affymetrix.com/support/mas/index.affx > > then "Select a product" e.g. HuExon array, > > then check "Software & Data" i.e. "Annotation Files" and > "Library Files" > > then click "Go". > > The resulting page contains "Current NetAffx Annotation Files" which > > contains both the transcript and probeset annotation files. > > Not that the following is guaranteed to be robust to affy file > movement, but > > library(AffyCompatible) > rsrc <- NetAffxResource("your at username", "password") > names(rsrc) > rsrc[["HuEx-1_0-st-v2"]] > rsrc[["HuEx-1_0-st-v2"]][[1]]] > sapply(affxAnnotation(rsrc[["HuEx-1_0-st-v2"]]), affxDescription) > anno <- affxFile(rsrc[["HuEx-1_0-st-v2", > "Probeset Annotations, CSV Format"]]) > csv <- readAnnotation(rsrc, annotation=anno) > > The vignette "Annotation retrieval with NetAffxResource" is a useful > starting place. > > Martin > > > > > > > Best regards > > Christian > > > > > > Steve Shen wrote: > >> Dear Christian, > >> > >> A quick question about creating scheme files, I am trying to > download > >> 'transcripts.cvs' and 'probeset.cvs' files from > >> > http://www.affymetrix.com/support/technical/annotationfilesmain. affx?hightlight=true&rootCategoryId= > <http: www.affymetrix.com="" support="" technical="" annotationfilesmain="" .affx?hightlight="true&amp;rootCategoryId="> > >> > <http: www.affymetrix.com="" support="" technical="" annotationfilesmain="" .affx?hightlight="true&amp;rootCategoryId="> <http: www.affymetrix.com="" support="" technical="" annotationfilesmain="" .affx?hightlight="true&amp;rootCategoryId=">>. > >> It seemed to be that only transcripts.cvs available from affy site. > >> Can you or someone else point me out where to find the files? > Thanks, > >> > >> Steve > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor at stat.math.ethz.ch > <mailto: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 > > > -- > Martin Morgan > Computational Biology / Fred Hutchinson Cancer Research Center > 1100 Fairview Ave. N. > PO Box 19024 Seattle, WA 98109 > > Location: Arnold Building M1 B861 > Phone: (206) 667-2793 > >
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Dear Christian, Having a centralized scheme file repository will at least allow people to stay on same page and make trouble shooting easier, I think. I can make an effort and find a place to host these files. Give me a little time please, I will let you know what happens. Thanks, Steve On Sun, Mar 7, 2010 at 4:28 PM, cstrato <cstrato@aon.at> wrote: > Dear Steve, > > In principle I can create the scheme files for the mostly used arrays > (since I do it anyhow for testing purposes), the only question is where to > upload the scheme files. > > > Best regards > Christian > > Steve Shen wrote: > >> Dear Christian and Martin, >> >> Thanks so much for your help. I got what I wanted. However, will that be >> possible for xps users to have a scheme file repository? It might be two >> much work for your team. Thanks again, >> >> Steve >> >> On Sun, Mar 7, 2010 at 3:19 PM, Martin Morgan <mtmorgan@fhcrc.org<mailto:>> mtmorgan@fhcrc.org>> wrote: >> >> On 03/07/2010 11:59 AM, cstrato wrote: >> > Dear Steve, >> > >> > For some reason Affymetrix has reorganized their web-site in a >> way so >> > that it is really hard to find anything!! >> > >> > As far as I can see, go to: >> > http://www.affymetrix.com/support/mas/index.affx >> > then "Select a product" e.g. HuExon array, >> > then check "Software & Data" i.e. "Annotation Files" and >> "Library Files" >> > then click "Go". >> > The resulting page contains "Current NetAffx Annotation Files" which >> > contains both the transcript and probeset annotation files. >> >> Not that the following is guaranteed to be robust to affy file >> movement, but >> >> library(AffyCompatible) >> rsrc <- NetAffxResource("your@username", "password") >> names(rsrc) >> rsrc[["HuEx-1_0-st-v2"]] >> rsrc[["HuEx-1_0-st-v2"]][[1]]] >> sapply(affxAnnotation(rsrc[["HuEx-1_0-st-v2"]]), affxDescription) >> anno <- affxFile(rsrc[["HuEx-1_0-st-v2", >> "Probeset Annotations, CSV Format"]]) >> csv <- readAnnotation(rsrc, annotation=anno) >> >> The vignette "Annotation retrieval with NetAffxResource" is a useful >> starting place. >> >> Martin >> >> >> >> > >> > Best regards >> > Christian >> > >> > >> > Steve Shen wrote: >> >> Dear Christian, >> >> >> >> A quick question about creating scheme files, I am trying to >> download >> >> 'transcripts.cvs' and 'probeset.cvs' files from >> >> >> >> http://www.affymetrix.com/support/technical/annotationfilesmain.aff x?hightlight=true&rootCategoryId= >> < >> http://www.affymetrix.com/support/technical/annotationfilesmain.aff x?hightlight=true&rootCategoryId= >> > >> >> >> < >> http://www.affymetrix.com/support/technical/annotationfilesmain.aff x?hightlight=true&rootCategoryId= >> < >> http://www.affymetrix.com/support/technical/annotationfilesmain.aff x?hightlight=true&rootCategoryId= >> >>. >> >> It seemed to be that only transcripts.cvs available from affy site. >> >> Can you or someone else point me out where to find the files? >> Thanks, >> >> >> >> Steve >> > >> > _______________________________________________ >> > Bioconductor mailing list >> > Bioconductor@stat.math.ethz.ch >> <mailto:bioconductor@stat.math.ethz.ch> >> >> > https://stat.ethz.ch/mailman/listinfo/bioconductor >> > Search the archives: >> > http://news.gmane.org/gmane.science.biology.informatics.conductor >> >> >> -- >> Martin Morgan >> Computational Biology / Fred Hutchinson Cancer Research Center >> 1100 Fairview Ave. N. >> PO Box 19024 Seattle, WA 98109 >> >> Location: Arnold Building M1 B861 >> Phone: (206) 667-2793 >> >> >> > [[alternative HTML version deleted]]
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Dear Martin, Thank you for this interesting alternative, however it requires an Affymetrix account, while you can currently download the annotation files from the Affymetrix website w/o account (currently you need an account only to download the library files). Best regards Christian Martin Morgan wrote: > On 03/07/2010 11:59 AM, cstrato wrote: > >> Dear Steve, >> >> For some reason Affymetrix has reorganized their web-site in a way so >> that it is really hard to find anything!! >> >> As far as I can see, go to: >> http://www.affymetrix.com/support/mas/index.affx >> then "Select a product" e.g. HuExon array, >> then check "Software & Data" i.e. "Annotation Files" and "Library Files" >> then click "Go". >> The resulting page contains "Current NetAffx Annotation Files" which >> contains both the transcript and probeset annotation files. >> > > Not that the following is guaranteed to be robust to affy file movement, but > > library(AffyCompatible) > rsrc <- NetAffxResource("your at username", "password") > names(rsrc) > rsrc[["HuEx-1_0-st-v2"]] > rsrc[["HuEx-1_0-st-v2"]][[1]]] > sapply(affxAnnotation(rsrc[["HuEx-1_0-st-v2"]]), affxDescription) > anno <- affxFile(rsrc[["HuEx-1_0-st-v2", > "Probeset Annotations, CSV Format"]]) > csv <- readAnnotation(rsrc, annotation=anno) > > The vignette "Annotation retrieval with NetAffxResource" is a useful > starting place. > > Martin > > > > >> Best regards >> Christian >> >> >> Steve Shen wrote: >> >>> Dear Christian, >>> >>> A quick question about creating scheme files, I am trying to download >>> 'transcripts.cvs' and 'probeset.cvs' files from >>> http://www.affymetrix.com/support/technical/annotationfilesmain.af fx?hightlight=true&rootCategoryId= >>> <http: www.affymetrix.com="" support="" technical="" annotationfilesmain.a="" ffx?hightlight="true&amp;rootCategoryId=">. >>> It seemed to be that only transcripts.cvs available from affy site. >>> Can you or someone else point me out where to find the files? Thanks, >>> >>> Steve >>> >> _______________________________________________ >> 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 >> > > >
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An account is free.... ________________________________________ From: bioconductor-bounces@stat.math.ethz.ch [bioconductor- bounces@stat.math.ethz.ch] On Behalf Of cstrato [cstrato@aon.at] Sent: 07 March 2010 21:12 To: Martin Morgan Cc: Bioconductor at stat.math.ethz.ch Subject: Re: [BioC] where to download 'probeset.cvs' file for creating scheme file Dear Martin, Thank you for this interesting alternative, however it requires an Affymetrix account, while you can currently download the annotation files from the Affymetrix website w/o account (currently you need an account only to download the library files). Best regards Christian Martin Morgan wrote: > On 03/07/2010 11:59 AM, cstrato wrote: > >> Dear Steve, >> >> For some reason Affymetrix has reorganized their web-site in a way so >> that it is really hard to find anything!! >> >> As far as I can see, go to: >> http://www.affymetrix.com/support/mas/index.affx >> then "Select a product" e.g. HuExon array, >> then check "Software & Data" i.e. "Annotation Files" and "Library Files" >> then click "Go". >> The resulting page contains "Current NetAffx Annotation Files" which >> contains both the transcript and probeset annotation files. >> > > Not that the following is guaranteed to be robust to affy file movement, but > > library(AffyCompatible) > rsrc <- NetAffxResource("your at username", "password") > names(rsrc) > rsrc[["HuEx-1_0-st-v2"]] > rsrc[["HuEx-1_0-st-v2"]][[1]]] > sapply(affxAnnotation(rsrc[["HuEx-1_0-st-v2"]]), affxDescription) > anno <- affxFile(rsrc[["HuEx-1_0-st-v2", > "Probeset Annotations, CSV Format"]]) > csv <- readAnnotation(rsrc, annotation=anno) > > The vignette "Annotation retrieval with NetAffxResource" is a useful > starting place. > > Martin > > > > >> Best regards >> Christian >> >> >> Steve Shen wrote: >> >>> Dear Christian, >>> >>> A quick question about creating scheme files, I am trying to download >>> 'transcripts.cvs' and 'probeset.cvs' files from >>> http://www.affymetrix.com/support/technical/annotationfilesmain.af fx?hightlight=true&rootCategoryId= >>> <http: www.affymetrix.com="" support="" technical="" annotationfilesmain.a="" ffx?hightlight="true&amp;rootCategoryId=">. >>> It seemed to be that only transcripts.cvs available from affy site. >>> Can you or someone else point me out where to find the files? Thanks, >>> >>> Steve >>> >> _______________________________________________ >> 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 >> > > > _______________________________________________ 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
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