[BioC] where to download 'probeset.cvs' file for creating scheme file

[cstrato]

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&rootCategoryId=>
>     >>
>     <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
>     >
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>
>     --
>     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
>
>