[BioC] Create affyBatch from mouse exon array data using ReadAffy or extractAffyBatch() from aroma.affymetrix

[Martin Morgan]

Mark Robinson <mrobinson at wehi.EDU.AU> writes:

> Hi An.
>
>> With respect to xps, your reference to script4xps.R is really
>> helpful.  Do you have a URL from where the files "MoEx-1_0-st- 
>> v1.r2.clf", "MoEx-1_0-st-v1.r2.pgf", "MoEx-1_0-st- 
>> v1.na25.mm9.probeset.csv", "MoEx-1_0-st-v1.na25.mm9.transcript.csv"
>> can be downloaded?  I searched on the Affy site but did not find it,
>> sorry.
>
> To answer this part of your question, you can get the probeset.csv
> file from:
> http://www.affymetrix.com/analysis/downloads/current_exon/
>
> The PGF/CLF can be found at:
> http://www.affymetrix.com/support/technical/libraryfilesmain.affx
>
> Look for "Mouse Exon 1.0 ST Array Analysis (zip, 114 MB)", which after
> logging in, will get you:
> MoEx-1_0-st-v1.r2.zip

A relatively new interface to managing these files is in the
AffyCompatible package. It requires that you've registered on the
NetAffx site, and that you know your Affx Licence (usually specific to
your organization; usually an email to affy tech support gets you
this). You can then start a session

> rsrc <- NetAffxResource("mtmorgan at fhcrc.org", password, affxLicence)
> rsrc
directory: /tmp/RtmpBakrNp
annotationsFile: NetAffxAnnotFileList.xml
affxUrl: https://www.affymetrix.com/analysis/downloads/netaffxapi/GetFileList.jsp
affxLicence: ********
user: mtmorgan at fhcrc.org
password: ********

discover available chips, their annotations, and file details 

> names(rsrc)
...
 [75] "Mm_PromP"                       "MoEx-1_0-st-v1"                
...
> names(rsrc[["MoEx-1_0-st-v1"]])
 [1] "Probe Sequences, FASTA format"             
 [2] "Probe Sequences, tabular format"           
 [3] "Probeset Annotations, CSV Format"          
 [4] "Transcript Cluster Annotations, CSV"       
 [5] "Transcript Cluster Sequences, FASTA format"
 [6] "Background Probes File"                    
 [7] "Intensity Layout File"                     
 [8] "EC Default Analysis Specifications"        
 [9] "Meta Probeset File"                        
[10] "Probe Group File"                          
[11] "Probeset List File"                        
[12] "QC Control File"                           
> anno <- rsrc[["MoEx-1_0-st-v1", "Probe Group File"]]
> anno
affxType: pgf 
affxDescription: Probe Group File 
affxFile: AffxFile(1)

and retrieve the file (to 'directory' of resource; you'll likely want
to specify directory when creating rsrc)

> readAnnotation(rsrc, annotation=anno)
trying URL 'http://www.affymetrix.com/analysis/downloads/na20/exon/MoEx-1_0-st-v1.r2.pgf.zip'
Content type 'application/zip' length 84438153 bytes (80.5 Mb)
opened URL
==================================================
downloaded 80.5 Mb

returning path to file of affxType 'pgf'
[1] "/tmp/RtmpBakrNp/MoEx-1_0-st-v1.r2.pgf.zip"

The vignette NetAffxResource is the best place for more information.

Martin

> There are plans to make a couple versions of Mouse CDFs for use with
> FIRMA within aroma.affymetrix.  I'm not sure when that will actually
> be, but hopefully "soon".
>
>
>> Does xps work with AffyBatches?  If not, is it possible to create an
>> AffyBatch with the raw data?
>
>
> xps, from my limited experience with, does not deal directly with
> AffyBatch objects, but maybe you can export one.
>
> Cheers,
> Mark
>
>
>
> ------------------------------
> Mark Robinson
> Epigenetics Laboratory, Garvan
> Bioinformatics Division, WEHI
> e: m.robinson at garvan.org.au
> e: mrobinson at wehi.edu.au
> p: +61 (0)3 9345 2628
> f: +61 (0)3 9347 0852
>
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-- 
Martin Morgan
Computational Biology / Fred Hutchinson Cancer Research Center
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