Hey, Michal - Perhaps try norm.type='pmonly' n the call to justPlier()? Cordially, - Jeremy On Mon, Dec 13, 2010 at 11:48 PM, Hooiveld, Guido <guido.hooiveld@wur.nl>wrote: > Hi Michal, > > These functions will never work because the ST arrays do not contain any > mismatch probes, which are required for MAS5, GCRMA and PLIER. In other > words, these are PM (perfect match) only arrays that can be normalized with > e.g. RMA or VSN. > > HTH, > 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 > internet: http://nutrigene.4t.com > email: guido.hooiveld@wur.nl > > > > > -----Original Message----- > > From: bioconductor-bounces@r-project.org > > [mailto:bioconductor-bounces@r-project.org] On Behalf Of > > Michal Blazejczyk > > Sent: Tuesday, December 14, 2010 05:53 > > To: bioconductor@r-project.org > > Subject: [BioC] affy package and ST arrays > > > > Dear list, > > > > I have a question. I've noticed that The most recent > > Biocinductor version contains CDF packages for Affymetrix's ST arrays. > > > > As a result, functions such as rma() or just.rma() now work > > well with these arrays, which is great. > > > > However, many other normalization functions (e.g. gcrma(), > > mas5(), mas5calls.AffyBatch(), or justPlier()) are still > > throwing errors. > > > > Does anybody know if there are plans to make these other > > methods work with the CDF packages for ST arrays? > > > > Best regards, > > > > Michal Blazejczyk > > FlexArray Lead Developer > > McGill University and Genome Quebec Innovation Centre > > 514-398-4400 x09625 http://genomequebec.mcgill.ca/FlexArray > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor@r-project.org > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > Search the archives: > > http://news.gmane.org/gmane.science.biology.informatics.conductor > > > > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > -- Jeremy Gollub jeremy@gollub.net [[alternative HTML version deleted]]

Hi Michal I'm not sure it's correct to say that GCRMA can't be applied to GeneST data. The gcrma package allows one to specify negative control probes to estimate probe affinity, rather than using MM probes. Unfortunately it fails with the annotation packages in BioConductor due to some probes not having length 25. I've put some details on how I built an alternative pair of annotation packages (along with the packages them selves) here: http://www.compbio.group.cam.ac.uk/Resources/GeneST/ <http: www.compbio.group.cam.ac.uk="" resources="" genest=""/>I hope that it's of some use -- Mike Smith PhD Student Computational Biology Group Cambridge University On Tue, Dec 14, 2010 at 7:48 AM, Hooiveld, Guido <guido.hooiveld@wur.nl>wrote: > Hi Michal, > > These functions will never work because the ST arrays do not contain any > mismatch probes, which are required for MAS5, GCRMA and PLIER. In other > words, these are PM (perfect match) only arrays that can be normalized with > e.g. RMA or VSN. > > HTH, > 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 > internet: http://nutrigene.4t.com > email: guido.hooiveld@wur.nl > > > > > -----Original Message----- > > From: bioconductor-bounces@r-project.org > > [mailto:bioconductor-bounces@r-project.org] On Behalf Of > > Michal Blazejczyk > > Sent: Tuesday, December 14, 2010 05:53 > > To: bioconductor@r-project.org > > Subject: [BioC] affy package and ST arrays > > > > Dear list, > > > > I have a question. I've noticed that The most recent > > Biocinductor version contains CDF packages for Affymetrix's ST arrays. > > > > As a result, functions such as rma() or just.rma() now work > > well with these arrays, which is great. > > > > However, many other normalization functions (e.g. gcrma(), > > mas5(), mas5calls.AffyBatch(), or justPlier()) are still > > throwing errors. > > > > Does anybody know if there are plans to make these other > > methods work with the CDF packages for ST arrays? > > > > Best regards, > > > > Michal Blazejczyk > > FlexArray Lead Developer > > McGill University and Genome Quebec Innovation Centre > > 514-398-4400 x09625 http://genomequebec.mcgill.ca/FlexArray > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor@r-project.org > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > Search the archives: > > http://news.gmane.org/gmane.science.biology.informatics.conductor > > > > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > [[alternative HTML version deleted]]