[BioC] cdf.file for Affymetrix Rat Gene 1.1 ST Array Plate

[Hooiveld, Guido]

Hi Oksana,

Let me first say this: as many ppl have said on his list, the preferred workflow for the analyses of Gene ST arrays is by using the libraries 'oligo' or 'xps'; both provide you an integrated workflow directly using the files provided by Affymetrix to analyse these type of arrays.
http://www.bioconductor.org/help/workflows/oligo-arrays/#pre-processing-resources


Having said this, let me answer (part of) your questions: No, you cannot use the CDF file for the Gene 1.0 ST array to analyse the Gene 1.1 ST arrays! However, you may be interested in this thread:
http://article.gmane.org/gmane.science.biology.informatics.conductor/32256
and this notification regarding aroma.affymetrix: 
"Version: 1.8.3 [2011-01-09]
o Added writeCdf() for AffyGenePDInfo, which replaces pdInfo2Cdf().
  An auxillary CEL file is no longer needed to create a CDF from
  an PDInfo package.  Moreover, contrary pdInfo2Cdf(), the generated
  CDF now gets a correct/formal Affymetrix chip type."
http://cran.r-project.org/web/packages/aroma.affymetrix/NEWS

I haven't used the annotation packages you mention, but I *assume* you could use them depending on the CDF you use (gene or transcript-centric).

HTH to get you started,
Guido


------------------------------------------------ 
Guido Hooiveld, PhD 
Nutrition, Metabolism & Genomics Group 
Division of Human Nutrition 
Wageningen University 
Biotechnion, Bomenweg 2 
NL-6703 HD Wageningen 
the Netherlands 
tel: (+)31 317 485788 
fax: (+)31 317 483342 
email:      guido.hooiveld at wur.nl
internet:   http://nutrigene.4t.com 
http://www.researcherid.com/rid/F-4912-2010


> -----Original Message-----
> From: bioconductor-bounces at r-project.org 
> [mailto:bioconductor-bounces at r-project.org] On Behalf Of korobko
> Sent: Tuesday, January 18, 2011 15:37
> To: bioconductor at r-project.org
> Subject: [BioC] cdf.file for Affymetrix Rat Gene 1.1 ST Array Plate
> 
> My name is Oksana Korobko and I'm Postdoc at LACDR, Leiden 
> University, the Netherlands. 
> 
> I do the statistical analysis of microarray data for 
> Affymetrix Rat Gene 1.1 ST Array Plate. For normalization I 
> need cdf, probe and df files. I cannot find the cdf and probe 
> files for this type of array. There are only cdf 
> (ragene10stv1cdf 
> <http://www.bioconductor.org/help/bioc-views/release/data/anno
tation/html/ra
> gene10stv1cdf.html> ) and probe (ragene10stv1probe 
> <http://www.bioconductor.org/help/bioc-views/release/data/anno
tation/html/ra
> gene10stv1probe.html> ) files for Affymetrix  Rat Gene 1.0 
> ST, but there are db.file for Affymetrix Rat Gene 1.1 ST 
> (ragene11stprobeset.db 
> <http://www.bioconductor.org/help/bioc-views/release/data/anno
tation/html/ra
> gene11stprobeset.db.html> ) and for Affymetrix Rat Gene 1.0 
> ST (ragene10stprobeset.db 
> <http://www.bioconductor.org/help/bioc-views/release/data/anno
tation/html/ra
> gene10stprobeset.db.html> ).
> 
> My question is: Can I use cdf and probe files from previous 
> version 1.0 ST to my Rat Gene 1.1 ST data? And if the 
> previouse answer is posistive, what db.file should I use for 
> 1.1 ST array ragene11stprobeset.db 
> <http://www.bioconductor.org/help/bioc-views/release/data/anno
tation/html/ra
> gene11stprobeset.db.html>  or ragene10stv1probe 
> <http://www.bioconductor.org/help/bioc-views/release/data/anno
tation/html/ra
> gene10stv1probe.html> ?
> 
>  
> 
> Many thanks in advance,
> 
> Oksana Korobko
> 
>  
> 
> 
> 	[[alternative HTML version deleted]]
> 
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