[BioC] where to download 'probeset.cvs' file for creating scheme file
cstrato at aon.at
Sun Mar 7 22:28:13 CET 2010
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.
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,
> 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
> rsrc <- NetAffxResource("your at username", "password")
> 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.
> > Best regards
> > Christian
> > Steve Shen wrote:
> >> Dear Christian,
> >> A quick question about creating scheme files, I am trying to
> >> 'transcripts.cvs' and 'probeset.cvs' files from
> >> 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?
> >> Steve
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> Martin Morgan
> Computational Biology / Fred Hutchinson Cancer Research Center
> 1100 Fairview Ave. N.
> PO Box 19024 Seattle, WA 98109
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