globaltest on cDNA

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Lang Chen ▴ 100

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ADD COMMENT • link updated 18.7 years ago by Oosting, J. PATH ▴ 550 • written 18.7 years ago by Lang Chen ▴ 100

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James W. MacDonald 67k

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Lang Chen wrote: > Dear all, > > > > I have cDNA chips( treatmean(cys5)/control(cys3)) and want to run > globaltest. Could anyone show me how to do this in the package of > globaltest? Have you looked at the vignette for this package? I think that might be a reasonable place to start. library(globaltest) openVignette() HTH, Jim > > > > Thank you for your help. > > > > Lang Chen > > Biostatistics > > Univ of Alabama at Birmingham > > > > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor -- James W. MacDonald University of Michigan Affymetrix and cDNA Microarray Core 1500 E Medical Center Drive 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.

ADD COMMENT • link 18.7 years ago James W. MacDonald 67k

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James W. MacDonald wrote: > Have you looked at the vignette for this package? I think > that might be > a reasonable place to start. > > library(globaltest) > openVignette() library(Biobase) library(globaltest) openVignette() might work better. Regards Gerhard

ADD REPLY • link 18.7 years ago Gerhard Thallinger ▴ 180

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Gerhard Thallinger wrote: > James W. MacDonald wrote: > > >>Have you looked at the vignette for this package? I think >>that might be >>a reasonable place to start. >> >>library(globaltest) >>openVignette() > > > library(Biobase) > library(globaltest) > openVignette() > > might work better. No, it will work identically. globaltest imports Biobase, so will automatically load Biobase. > library(globaltest) Loading required package: multtest Loading required package: Biobase <============= Loading required package: tools Welcome to Bioconductor Vignettes contain introductory material. To view, simply type 'openVignette()' or start with 'help(Biobase)'. For details on reading vignettes, see the openVignette help page. Loading required package: survival Loading required package: splines > > Regards > > Gerhard > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor -- 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

ADD REPLY • link 18.7 years ago James W. MacDonald 67k

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Quoting "James W. MacDonald" <jmacdon at="" med.umich.edu="">: >>> library(globaltest) >>> openVignette() >> >> library(Biobase) >> library(globaltest) >> openVignette() >> >> might work better. > > No, it will work identically. globaltest imports Biobase, so will > automatically load Biobase. This may be true for the development version of Bioconductor. The latest "stable" release (1.7) contains a version of globaltest where the require(Biobase) seems to be missing and an error message is displayed: > library(globaltest) > sessionInfo() R version 2.2.0, 2005-10-06, i386-pc-mingw32 attached base packages: [1] "methods" "stats" "graphics" "grDevices" "utils" "datasets" "base" other attached packages: globaltest "3.2.0" > openVignette() Error: couldn't find function "openVignette" Gerhard

ADD REPLY • link 18.7 years ago Gerhard Thallinger ▴ 180

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Oosting, J. PATH ▴ 550

@oosting-j-path-412

Last seen 10.2 years ago

I don't think the vignette will help you very far in this case. You haven't provided enough information to help you completely but I can sketch you a scenario. Ideally you will need an (Biobase) exprSet object with intensity data for both channels to perform the globaltest Read in your samples with limma and do proper normalizations. (read limma vignette on how to do this) You now have a MAList object, convert this with RG.MA() to an RGList object This object can be converted to an exprSet object using the convert package Eset<-as(RG,"exprSet") If you have 5 slides you can now perform a globaltest between the treated and controls with a command like this globaltest(Eset,c(1,0,1,0,1,0,1,0,1,0)) Jan Oosting -----Original Message----- From: bioconductor-bounces@stat.math.ethz.ch [mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of Lang Chen Sent: dinsdag 14 maart 2006 0:45 To: bioconductor at stat.math.ethz.ch Subject: [BioC] globaltest on cDNA Dear all, I have cDNA chips( treatmean(cys5)/control(cys3)) and want to run globaltest. Could anyone show me how to do this in the package of globaltest? Thank you for your help. Lang Chen Biostatistics Univ of Alabama at Birmingham [[alternative HTML version deleted]] _______________________________________________ Bioconductor mailing list Bioconductor at stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/bioconductor

ADD COMMENT • link 18.7 years ago Oosting, J. PATH ▴ 550

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