How to load .gpr file into bioconductor?
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@lhmaontuedutw-595
Last seen 9.6 years ago
Dear friends: Apologize for a novice asking a basic question. Could somebody please tell me how to load a .gpr or the GenePix result into Bioconductor? Or any place having documents about this answer? I noticed that there is a tutorial document using the demo example-swirl. How could I pack several microarray result files into a package like swirl, or could I load the raw .gpr directly into bioconductor? Thank you for your answer. Sincerely, Erik
Microarray Microarray • 2.7k views
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@wolfgang-huber-3550
Last seen 3 months ago
EMBL European Molecular Biology Laborat…
Hi Erik, this is a fairly basic task, and a quick browse with google resulted in at least three ways to do it (they are all more or less equivalent) the function "read.Genepix" in package marrayInput the function "readImageFiles" in the package arrayMagic the function "read.maimages" in limma Have a look at the respective package vignettes for more details. Best wishes Wolfgang ------------------------------------- Wolfgang Huber Division of Molecular Genome Analysis German Cancer Research Center Heidelberg, Germany Phone: +49 6221 424709 Fax: +49 6221 42524709 Http: www.dkfz.de/abt0840/whuber ------------------------------------- On Sun, 11 Jan 2004 lhmao@ntu.edu.tw wrote: > Dear friends: > Apologize for a novice asking a basic question. Could somebody please tell me > how to load a .gpr or the GenePix result into Bioconductor? Or any place having > documents about this answer? I noticed that there is a tutorial document using > the demo example-swirl. How could I pack several microarray result files into a > package like swirl, or could I load the raw .gpr directly into bioconductor? > Thank you for your answer. > Sincerely, > Erik > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor >
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Hi Erik, Just to add, you can also try gpTools(raw=TRUE) from marrayTools package. Jean ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Jean Yee Hwa Yang jean@biostat.ucsf.edu Division of Biostatistics, Tel: (415) 476-3368 University of California, Fax: (415) 476-6014 500 Parnassus Avenue, MU 420-W, San Francisco, CA 94143-0560 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ On Mon, 12 Jan 2004 w.huber@dkfz-heidelberg.de wrote: > Hi Erik, > > this is a fairly basic task, and a quick browse with google resulted in at > least three ways to do it (they are all more or less equivalent) > > the function "read.Genepix" in package marrayInput > the function "readImageFiles" in the package arrayMagic > the function "read.maimages" in limma > > Have a look at the respective package vignettes for more details. > > Best wishes > Wolfgang > > ------------------------------------- > Wolfgang Huber > Division of Molecular Genome Analysis > German Cancer Research Center > Heidelberg, Germany > Phone: +49 6221 424709 > Fax: +49 6221 42524709 > Http: www.dkfz.de/abt0840/whuber > ------------------------------------- > > On Sun, 11 Jan 2004 lhmao@ntu.edu.tw wrote: > > > Dear friends: > > Apologize for a novice asking a basic question. Could somebody please tell me > > how to load a .gpr or the GenePix result into Bioconductor? Or any place having > > documents about this answer? I noticed that there is a tutorial document using > > the demo example-swirl. How could I pack several microarray result files into a > > package like swirl, or could I load the raw .gpr directly into bioconductor? > > Thank you for your answer. > > Sincerely, > > Erik > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor@stat.math.ethz.ch > > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor > > > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor >
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@james-w-macdonald-5106
Last seen 32 minutes ago
United States
Probably the easiest way is to use limma. There is a very detailed manual that comes with this package that explains exactly what you need to do. You can access the manual at the top of the html help page for limma under 'overview' or some such thing (I am at home and don't have R installed here). I would also recommend using limma for your data analysis. The learning curve might be a bit steep, but there are several examples in the manual that you can use to help you figure out how to do things. HTH, Jim James W. MacDonald Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109 734-647-5623 >>> <lhmao@ntu.edu.tw> 01/11/04 6:02 AM >>> Dear friends: Apologize for a novice asking a basic question. Could somebody please tell me how to load a .gpr or the GenePix result into Bioconductor? Or any place having documents about this answer? I noticed that there is a tutorial document using the demo example-swirl. How could I pack several microarray result files into a package like swirl, or could I load the raw .gpr directly into bioconductor? Thank you for your answer. Sincerely, Erik _______________________________________________ Bioconductor mailing list Bioconductor@stat.math.ethz.ch https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor
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