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="" annotation="" html="" ra="" gene10stv1cdf.html=""> ) and probe (ragene10stv1probe <http: www.bioconductor.org="" help="" bioc-="" views="" release="" data="" annotation="" 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="" annotation="" html="" ra="" gene11stprobeset.db.html=""> ) and for Affymetrix Rat Gene 1.0 ST (ragene10stprobeset.db <http: www.bioconductor.org="" help="" bioc-="" views="" release="" data="" annotation="" 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="" annotation="" html="" ra="" gene11stprobeset.db.html=""> or ragene10stv1probe <http: www.bioconductor.org="" help="" bioc-="" views="" release="" data="" annotation="" html="" ra="" gene10stv1probe.html=""> ? Many thanks in advance, Oksana Korobko [[alternative HTML version deleted]]

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/3 2256 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]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > >