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

[cstrato]

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.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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>>     
>
>
>