AffyQCReport: "I'm sorry, I do not know about chip type" (celeganscdf)
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Emmanuel Levy ▴ 270
@emmanuel-levy-1240
Last seen 7.0 years ago
Hello, I have an error with affyQCReport: Error in qc.affy(unnormalised, ...) : I'm sorry, I do not know about chip type: celeganscdf Error in plot(qc(object)) : unable to find the argument 'x' in selecting a method for function 'plot' The reason is that the package of the chip I use (celegans) is not found in .qcEnv Do you know why it is not added when I load the celeganscdf library? Shall I add it myself? If yes could you please let me know how? Thanks in advance, Emmanuel > sessionInfo() R version 2.2.1, 2005-12-20, x86_64-redhat-linux-gnu attached base packages: [1] "splines" "tools" "methods" "stats" "graphics" "grDevices" [7] "utils" "datasets" "base" other attached packages: celeganscdf affyQCReport simpleaffy genefilter survival reposTools "1.10.0" "1.8.0" "2.4.2" "1.8.0" "2.20" "1.8.0" affy Biobase "1.8.1" "1.8.0"
cdf genefilter affy simpleaffy affyQCReport cdf genefilter affy simpleaffy affyQCReport • 1.2k views
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Seth Falcon ★ 7.4k
@seth-falcon-992
Last seen 10.3 years ago
Hi Emmanuel, "Emmanuel Levy" <emmanuel.levy at="" gmail.com=""> writes: > The reason is that the package of the chip I use (celegans) is not > found in .qcEnv > > Do you know why it is not added when I load the celeganscdf library? > Shall I add it myself? If yes could you please let me know how? > > Thanks in advance, > > Emmanuel > >> sessionInfo() > R version 2.2.1, 2005-12-20, x86_64-redhat-linux-gnu ^^^^^ That's a fairly old version of R (and hence you have rather old versions of the relevant BioC packages). Could you try updating to R 2.4.1, reinstalling BioC packages, and seeing if that resolves the issue? If not, at least you will be a on a more up-to-date version and it will be easier for the developers to respond to your bug reports/feature requests. + seth
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Updating may not solve your problem in this case - simpleaffy only has the control probe information for some common-used chips stored in it's environment; it doesn't take them from the cdf. There have been quite a few posts about this on the Bioconductor list... so many that it would be useful to put some sort of caveat in the help files for affyQCReport and simpleaffy! At any rate, check out my previous post and the possible fix referenced in it: https://stat.ethz.ch/pipermail/bioconductor/2007-January/015575.html Cheers, Jenny At 10:32 AM 2/6/2007, Seth Falcon wrote: >Hi Emmanuel, > >"Emmanuel Levy" <emmanuel.levy at="" gmail.com=""> writes: > > The reason is that the package of the chip I use (celegans) is not > > found in .qcEnv > > > > Do you know why it is not added when I load the celeganscdf library? > > Shall I add it myself? If yes could you please let me know how? > > > > Thanks in advance, > > > > Emmanuel > > > >> sessionInfo() > > R version 2.2.1, 2005-12-20, x86_64-redhat-linux-gnu > ^^^^^ > >That's a fairly old version of R (and hence you have rather old >versions of the relevant BioC packages). > >Could you try updating to R 2.4.1, reinstalling BioC packages, and >seeing if that resolves the issue? If not, at least you will be a on >a more up-to-date version and it will be easier for the developers to >respond to your bug reports/feature requests. > >+ seth > >_______________________________________________ >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 Jenny Drnevich, Ph.D. Functional Genomics Bioinformatics Specialist W.M. Keck Center for Comparative and Functional Genomics Roy J. Carver Biotechnology Center University of Illinois, Urbana-Champaign 330 ERML 1201 W. Gregory Dr. Urbana, IL 61801 USA ph: 217-244-7355 fax: 217-265-5066 e-mail: drnevich at uiuc.edu
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Crispin Miller ★ 1.1k
@crispin-miller-264
Last seen 10.3 years ago
Hi, I've added these two chips to the devl version of simpleaffy - the update should appear on the website at some stage soon. All the best, Crispin -------------------------------------------------------- This email is confidential and intended solely for the use o...{{dropped}}
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