Hi Rainer, FYI there's a new version of bgx called mmbgx, available from http://bgx.org.uk (though not in bioconductor yet), which works with Gene ST arrays. Regards, Ernest On 15 Jun 2010, at 12:35, "Groot, Philip de" <philip.degroot at="" wur.nl=""> wrote: > Hello Rainer, > > Why don't you simply use vsnrma? This works perfectly fine for Gene > ST arrays! > This function resides in the vsn library. > > Regards, > > Dr. Philip de Groot Ph.D. > Bioinformatics Researcher > > Wageningen University / TIFN > Nutrigenomics Consortium > Nutrition, Metabolism & Genomics Group > Division of Human Nutrition > PO Box 8129, 6700 EV Wageningen > Visiting Address: Erfelijkheidsleer: De Valk, Building 304 > Dreijenweg 2, 6703 HA Wageningen > Room: 0052a > T: +31-317-485786 > F: +31-317-483342 > E-mail: Philip.deGroot at wur.nl > Internet: http://www.nutrigenomicsconsortium.nl > http://humannutrition.wur.nl/ > https://madmax.bioinformatics.nl/ > ________________________________________ > From: Richard Pearson [richard.pearson at well.ox.ac.uk] > Sent: 14 June 2010 15:08 > To: Rainer Tischler > Cc: bioconductor at stat.math.ethz.ch > Subject: Re: [BioC] gc-rma and vsn normalization for rat microarray > data > > Rainer > > Unfortunately you're not going to be able to use puma as the methods > require both perfect > match (PM) and mismatch (MM) data (and exon arrays have only the PM). > > Best wishes > > Richard > > Benilton Carvalho wrote: >> Rainer, >> >> I understand I don't offer a vsn() method in oligo (yet), but this >> can >> be easily achieved... Something like the following may get you >> started: >> >> library(oligo) >> cels = list.celfiles() >> raw = read.celfiles(cels) >> pms = pm(raw) >> pmsVSN = vsn::vsnMatrix(pms) >> pm(raw) <- pmVSN >> rm(pms, pmsVSN) >> >> If any of the other packages offer you a way of normalizing the data >> straight from the PM matrices, you can do as I show above... >> >> b >> >> >> On 11 June 2010 16:20, Rainer Tischler <rainer_t62 at="" yahoo.de=""> wrote: >>> Dear all, >>> >>> I am analyzing microarray data from an Affymetrix GeneChip Rat ST >>> 1.0 platform, however, since there is no annotation package >>> available that is compatible with the R-package "affy", so far I >>> have only been able to normalize the data using the simple RMA >>> method from the oligo-package. I would like to apply more advanced >>> normalization methods like GC-RMA, VSN, PUMA or BGX, but none of >>> these methods seems to be compatible with the oligo-package. >>> Is anybody aware of a possibility to analyze Affymetrix Rat data >>> with the standard affy-package, or alternatively, a possibility to >>> use any of the above normalization methods with the oligo-package? >>> >>> Many thanks, >>> Rainer >>> >>> >>> >>> _______________________________________________ >>> Bioconductor mailing list >>> Bioconductor at stat.math.ethz.ch >>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >>> >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >> > > -- > Dr Richard D Pearson richard.pearson at well.ox.ac.uk > Wellcome Trust Centre for Human Genetics http://www.well.ox.ac.uk/~rpearson > University of Oxford Tel: +44 (0)1865 617890 > Roosevelt Drive Mob: +44 (0)7971 221181 > Oxford OX3 7BN, UK Fax: +44 (0)1865 287664 > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor