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

[michael watson (IAH-C)]

An account is free....
________________________________________
From: bioconductor-bounces at stat.math.ethz.ch [bioconductor-bounces at stat.math.ethz.ch] On Behalf Of cstrato [cstrato at aon.at]
Sent: 07 March 2010 21:12
To: Martin Morgan
Cc: Bioconductor at stat.math.ethz.ch
Subject: Re: [BioC] where to download 'probeset.cvs' file for creating  scheme file

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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>
>
>

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