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]]