about the swirl data

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xpzhang ▴ 90

@xpzhang-780

Last seen 9.7 years ago

Hi,everybody! I am trying to learn how to use bioconductor to normalize my data. In R\rw1090\library\marrayInput\data, there are 7 files whose name is fish.gal, swirl.RData, swirl.1, swirl.2, swirl.3, swirl.4 and SwirlSample. I don't know how to make a *.RData using my own data.I read some document but have not found out how to do. Could anyone tell me? Thank you very much! -- Xiaopeng Zhang<xpzhang@genetics.ac.cn>

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ADD COMMENT • link updated 19.9 years ago by James Wettenhall ▴ 1000 • written 19.9 years ago by xpzhang ▴ 90

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witek ▴ 80

@witek-758

Last seen 9.7 years ago

Hi! .RData is a file in which R stores the session data. R generates it and stores all objects in the envirovment when you exit R. So my gues, as an R user not marrayInput user, is you have to do nothing. Sincerely Eryk *********** REPLY SEPARATOR *********** On 01.06.2004 at 15:45 xpzhang wrote: >Hi,everybody! > >I am trying to learn how to use bioconductor to normalize my data. In >R\rw1090\library\marrayInput\data, there are 7 files whose name is >fish.gal, swirl.RData, swirl.1, swirl.2, swirl.3, swirl.4 and >SwirlSample. I don't know how to make a *.RData using my own data.I read >some document but have not found out how to do. Could anyone tell me? > >Thank you very much! >-- >Xiaopeng Zhang<xpzhang@genetics.ac.cn> > >_______________________________________________ >Bioconductor mailing list >Bioconductor@stat.math.ethz.ch >https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor

ADD COMMENT • link 19.9 years ago witek ▴ 80

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On Tue, Jun 01, 2004 at 10:48:45AM +0200, witek wrote: > .RData is a file in which R stores the session data. R generates it and stores all objects in the envirovment when you exit R. So my gues, as an R user not marrayInput user, is you have to do nothing. In addition .Rdata is an often used ending (but not a required one) for R data objects. If you have one (or several) object(s) in R you may save them by > save(object, file="object.Rdata") and restore them by > load("object.Rdata") This is an easy way to make backups of huge R objects. I guess this is what has been done in the package. /Kasper > *********** REPLY SEPARATOR *********** > > On 01.06.2004 at 15:45 xpzhang wrote: > > >Hi,everybody! > > > >I am trying to learn how to use bioconductor to normalize my data. In > >R\rw1090\library\marrayInput\data, there are 7 files whose name is > >fish.gal, swirl.RData, swirl.1, swirl.2, swirl.3, swirl.4 and > >SwirlSample. I don't know how to make a *.RData using my own data.I read > >some document but have not found out how to do. Could anyone tell me? > > > >Thank you very much! > >-- > >Xiaopeng Zhang<xpzhang@genetics.ac.cn> > > > >_______________________________________________ > >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 -- Kasper Daniel Hansen, Research Assistant Department of Biostatistics, University of Copenhagen

ADD REPLY • link 19.9 years ago Kasper Daniel Hansen ▴ 630

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James Wettenhall ▴ 1000

@james-wettenhall-153

Last seen 9.7 years ago

Hi, > R\rw1090\library\marrayInput\data, there are 7 files whose name is In the marrayInput.pdf document in R\rw1090\library\marrayInput\doc\ the command: data(swirl) loads the swirl.RData file EARLY in the document, but this may be confusing because you WILL NOT have an .RData file BEFORE you start your microarray analysis. You have the option of saving your R session to an .RData file AFTER you have done some analysis. So just ignore the data(swirl) command in marrayInput.pdf for now (and ignore the following line showing the contents of the swirl object within R). You could also look at the limma package which demonstrates methods of reading two-color array data (including the swirl data set). In limma you would use read.maimages(...) instead of read.marrayRaw(...). The marrayInput package and marrayClasses, marrayNorm etc. have now been merged into one package, just called marray. So if you have a package called marrayInput, it may be out of date. Hope this helps, James ---------------------------------------------------------------------- ---- James Wettenhall Tel: (+61 3) 9345 2629 Division of Genetics and Bioinformatics Fax: (+61 3) 9347 0852 The Walter & Eliza Hall Institute E-mail: wettenhall@wehi.edu.au of Medical Research, Mobile: (+61 / 0 ) 438 527 921 1G Royal Parade, Parkville, Vic 3050, Australia http://www.wehi.edu.au

ADD COMMENT • link 19.9 years ago James Wettenhall ▴ 1000

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