Dear Christian,

Having a centralized scheme file repository will at least allow people to
stay on same page and make trouble shooting easier, I think. I can make an
effort and find a place to host these files. Give me a little time please, I
will let you know what happens.

Thanks,
Steve

On Sun, Mar 7, 2010 at 4:28 PM, cstrato <cstrato@aon.at> wrote:

> 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@fhcrc.org<mailto:
>> mtmorgan@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@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
>>    >
>>    > _______________________________________________
>>    > Bioconductor mailing list
>>    > Bioconductor@stat.math.ethz.ch
>>    <mailto:Bioconductor@stat.math.ethz.ch>
>>
>>    > https://stat.ethz.ch/mailman/listinfo/bioconductor
>>    > Search the archives:
>>    > http://news.gmane.org/gmane.science.biology.informatics.conductor
>>
>>
>>    --
>>    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
>>
>>
>>
>

	[[alternative HTML version deleted]]

