Using CDF file on affylmGUI
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@paul-christophschroder-1940
Last seen 8.1 years ago
Dear Bioconductor, I would like to use the affylmGUI but not with a chip from Bioconductor. The problem is, I have my own cdf-file and I want to use this one instead of the provided by Affymetrix. How should I go on? Many thanks in advance, Best, Paul C. Schr?der -- -- Paul C. Schr?der PhD Student Department for Proteomics & Bioinformatics Center for Applied Medicine (CIMA) Avda. P?o XII, 55 31008 Pamplona Tel. 948 194700 <pschrode at="" alumni.unav.es=""> ---------------------------------------------------------------- Este mensaje ha sido enviado desde https://webmail.unav.es
Proteomics GO affylmGUI Proteomics GO affylmGUI • 741 views
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@james-w-macdonald-5106
Last seen 21 hours ago
United States
Hi Paul, Paul Christoph Schr?der wrote: > Dear Bioconductor, > > I would like to use the affylmGUI but not with a chip from > Bioconductor. The problem is, I have my own cdf-file and I want to use > this one instead of the provided by Affymetrix. How should I go on? You will need to make a cdf package using the makecdfenv package. There is a vignette in makecdfenv that shows how to make a package, and then you should consult the 'Writing R Extensions' manual that comes with R, which shows how to install the package. Best, Jim > > Many thanks in advance, > > Best, > Paul C. Schr?der -- 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 ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues.
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@keith-satterley-1452
Last seen 7.9 years ago
Australia
Hi Paul, this feature has been asked for recently. The previous maintainer/programmer has gone some way down this path, but it is not functioning yet. I hope to look at this early in December. When it works I'll put it in the devel version of Bioconductor and let the list know, cheers, Keith ======================== Keith Satterley Bioinformatics Division The Walter and Eliza Hall Institute of Medical Research Parkville, Melbourne, Victoria, Australia ======================== Paul Christoph Schr?der wrote: > Dear Bioconductor, > > I would like to use the affylmGUI but not with a chip from > Bioconductor. The problem is, I have my own cdf-file and I want to use > this one instead of the provided by Affymetrix. How should I go on? > > Many thanks in advance, > > Best, > Paul C. Schr?der
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I am not too familiar with the affylmGUI package but I assume it builds on the structures from affy. In that case you should be able to do it manually: you make a cdf environment using "makecdfenv". You can either make a package like Jim is saying, which is better in the long run (but slightly more complicated especially on windows) or you can just have a cdf environment in your workspace. Then you need to link your data to this package. Presumably you have read in the data using affy, or perhaps using a GUI. Anyway, the data should bve in the form of an "AffyBatch" object. Say the data is called something like paulData. Then you just do R> paulData at cdfName <- "ENVNAME" with ENVNAME the name of your cdfenv. A slightly more explicit script would be something like R> customCdf <- makecdfenv(...) R> paulData <- ReadAffy(...) R> paulData at cdfName <- "customCdf" check by just doing a R> paulData If the cdfName has been set correctly and you have a cdf environment in your global workspace, the printing should work without problems. Kasper On Nov 18, 2006, at 3:15 AM, Keith Satterley wrote: > Hi Paul, > > this feature has been asked for recently. The previous maintainer/ > programmer has > gone some way down this path, but it is not functioning yet. I hope > to look at > this early in December. When it works I'll put it in the devel > version of > Bioconductor and let the list know, > > cheers, > > Keith > > ======================== > Keith Satterley > Bioinformatics Division > The Walter and Eliza Hall Institute of Medical Research > Parkville, Melbourne, > Victoria, Australia > ======================== > Paul Christoph Schr?der wrote: >> Dear Bioconductor, >> >> I would like to use the affylmGUI but not with a chip from >> Bioconductor. The problem is, I have my own cdf-file and I want to >> use >> this one instead of the provided by Affymetrix. How should I go on? >> >> Many thanks in advance, >> >> Best, >> Paul C. Schr?der > > _______________________________________________ > 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
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