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

[Martin Morgan]

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=>.
>> 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
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