gcRMA: problem compute.affinities.local on gngnf1musa
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Julien Roux ▴ 90
@julien-roux-2710
Last seen 4.8 years ago
Switzerland/Basel/University of Basel
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.conductor/ 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? 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
Annotation probe gcrma Annotation probe gcrma • 879 views
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@james-w-macdonald-5106
Last seen 4 hours ago
United States
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.conducto r/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 -- James W. MacDonald, M.S. Biostatistician Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109 734-647-5623
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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
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