Question: gc-rma and vsn normalization for rat microarray data
0
gravatar for Rainer Tischler
9.5 years ago by
Rainer Tischler60 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
ADD COMMENTlink modified 9.5 years ago by Benilton Carvalho4.3k • written 9.5 years ago by Rainer Tischler60
Answer: gc-rma and vsn normalization for rat microarray data
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gravatar for Benilton Carvalho
9.5 years ago by
Brazil/Campinas/UNICAMP
Benilton Carvalho4.3k 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 >
ADD COMMENTlink written 9.5 years ago by Benilton Carvalho4.3k
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
ADD REPLYlink written 9.5 years ago by Richard Pearson160
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@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
ADD REPLYlink written 9.5 years ago by Groot, Philip de630
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
ADD REPLYlink written 9.5 years ago by Ernest Turro30
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