Thanks Jim for this clear explanation. I will contact the authors of the method to get their comments on using compute.affinities() instead of compute.affinities.local() Regards, Julien James W. MacDonald a ?crit : > Hi Julien, > > Julien Roux wrote: >> Hello list, >> >> In *Schuster et al. 2007 (http://genomebiology.com/2007/8/6/R125) a >> method is presented allowing to correct *MAS5 present/absent calls >> based on gcRMA transformed PM threshold values. >> The R script is available in sup data at >> http://genomebiology.com/content/supplementary/gb-2007-8-6-r125-s1.txt >> >> When trying to run it on my data I am faced to an error: >> > data >> AffyBatch object >> size of arrays=854x854 features (11 kb) >> cdf=gnGNF1Musa (36182 affyids) >> number of samples=16 >> number of genes=36182 >> annotation=gngnf1musa >> notes= > ai <- compute.affinities.local(data, Array=NULL) >> Adjusting for optical effect................Done. >> Computing base-position profiles for probe affinitiesErreur dans >> complementSeq(seqs, start = 13, stop = 13) : >> Character N does not code for a nucleic acid. >> >> I tried with other platforms (e.g. mgu74av2) and this works. >> So I guess this is due to an error in the annotation package gngnf1musa. >> I installed this package (custom array affymetrix) made available by >> Cei Abreu-Goodger >> (http://article.gmane.org/gmane.science.biology.informatics.conduct or/13659) >> at ftp://ftp.sanger.ac.uk/pub/cei/gngnf1_R_packages.tar.gz >> What can be wrong? >> >> Then I tried: >> > ai <- compute.affinities(cdfName(data)) >> Computing affinities.Done. >> >> This worked. However I am not sure it is doing the same thing >> (Adjusting for optical effect? Computing base-position profiles for >> probe affinities?) >> What is the difference between compute.affinities and >> compute.affinities.local? > > From the source for these functions: > > ##this is almost the same as compute.affinities > ##except that affinity.spline.coefs is not loaded with data() > ##but computed using the data provided by the user > > So I have to assume that the probe package for your chip has some > probes in which Affy used the 'N' IUPAC symbol. Since gcrma doesn't > understand anything but ACTG, this causes the error. > > So when you use compute.affinities(), you load the pre-calculated > affinity data rather than using the sequences from your chip. Hence no > error. > > Best, > > Jim > > >> >> Thanks for your help to clarify this. >> Julien >> >> > sessionInfo() >> R version 2.7.0 (2008-04-22) >> i386-apple-darwin8.10.1 >> >> locale: >> C >> >> attached base packages: >> [1] splines tools stats graphics grDevices utils datasets >> [8] methods base other attached packages: >> [1] gngnf1musaprobe_1.8.1 gngnf1musacdf_1.14.0 gcrma_2.12.0 >> [4] matchprobes_1.12.0 affy_1.18.0 preprocessCore_1.2.0 >> [7] affyio_1.8.0 Biobase_2.0.1 > -- Julien Roux, PhD student http://www.unil.ch/dee/page22707.html Department of Ecology and Evolution Biophore, University of Lausanne, 1015 Lausanne, Switzerland tel: +41 21 692 4221 fax: +41 21 692 4165