mmm, after sending my previous email I noticed that the original affy cdf/sequence files are not aivalable at the U Michigan. I then realized my co-worker Philip de Groot has prepared a site a while ago at which all necessary files for the NuGO arrays are available. http://nugo-r.bioinformatics.nl/NuGO_R.html G > -----Original Message----- > From: Hooiveld, Guido > Sent: 13 December 2007 19:53 > To: 'H Parikh'; Bioconductor at stat.math.ethz.ch > Subject: RE: [BioC] Error in GCRMA package > > Hi Hemang, > > First, let me say that I don't know why you get this error > message using gcrma; that is something for the 'real' > gcrma-/R-experts... :-) > > However, our group has been involved in designing this array > (and the mouse one; NuGO = European Nutrigenomics > Organisation), and as a consequence we have quite some > experience with the analyses of these arrays. The default > (probe sequence + CDF) files provided by affymetrix, or the > remapped (custom) ones (kindly prepared by Manhong Dai et al > from U Michigan > [http://brainarray.mbni.med.umich.edu/Brainarray/Database/Cust > omCDF/CDF_download_v10.asp]) work always perfectly fine! So I > suggest to use the CDF files provided at the link above; I > guess one of the flavours must fit your needs... > > Regards, > 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 at wur.nl > > > > > -----Original Message----- > > From: bioconductor-bounces at stat.math.ethz.ch > > [mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf > Of H Parikh > > Sent: 13 December 2007 17:36 > > To: Bioconductor at stat.math.ethz.ch > > Subject: [BioC] Error in GCRMA package > > > > Dear All, > > > > I am getting a following error message when I tried to use gcrma > > package for a custom design affymetrix genechip. > > > > I made a nugohs1a520180cdf (custom Affymetrix chip) package using > > makecdfenv and also a nugohs1a520180cdfprobe package using > > matchprobes. > > > > >micro_data = ReadAffy() > > > > > micro_data at cdfName = "nugohs1a520180" > > > > >gcrma(micro_data) > > > > Adjusting for optical > > effect........................................................ > > ......................Done. > > > > Computing affinities.Done. > > > > Adjusting for non-specific binding.Error in pms[, i] <- > GSB.adj(Yin = > > pms[, i], subset = index.affinities, : > > > > number of items to replace is not a multiple of replacement length > > > > > > sessionInfo() > > > > R version 2.6.0 (2007-10-03) > > > > x86_64-unknown-linux-gnu > > > > other attached packages: > > > > gcrma_2.11.1 matchprobes_1.10.0 > > > > affy_1.16.0 preprocessCore_1.0.0 > > > > affyio_1.6.1 Biobase_1.16.2 > > > > > > I really appreciate your expert help in this matter. > > > > Thanks, > > > > Best regards, > > > > Hemang > > > > [[alternative HTML version deleted]] > > > > _______________________________________________ > > 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 > > > >