change working directory command on command line
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Tapan Mehta ▴ 270
@tapan-mehta-165
Last seen 9.7 years ago
Hello, i am trying to run Bioconductor on Unix. I am invoking R typing R on the command line. I believe there is no Gui available for the Unix version. It would be nice if somebody could tell me how to change the working directory on command line. Tapan Mehta
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Jeff Gentry ★ 3.9k
@jeff-gentry-12
Last seen 9.7 years ago
> i am trying to run Bioconductor on Unix. I am invoking > R typing R on the command line. I believe there is no > Gui available for the Unix version. It would be nice If you have gnome add a '--with=gnome' I believe it is, you can use the gnome R GUI: IE ./configure --enable-R-shlib make And then load R with: R --gui=gnome > if somebody could tell me how to change the working > directory on command line. setwd() and getwd() will get your current directory.
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John Zhang ★ 2.9k
@john-zhang-6
Last seen 9.7 years ago
If you mean changing directory from within R, then getwd() returns the working directory and setwd("your/working/dir") changes the working directory to your/working/dir. >Date: Fri, 6 Jun 2003 13:03:32 -0700 (PDT) >From: Tapan Mehta <tapmehta@yahoo.com> >To: bioconductor@stat.math.ethz.ch >MIME-Version: 1.0 >X-Virus-Scanned: by amavisd-milter (http://amavis.org/) >X-Virus-Scanned: by amavisd-milter (http://amavis.org/) >X-Spam-Status: No, hits=0.0 required=5.0 tests=none version=2.54 >X-Spam-Level: >X-Spam-Checker-Version: SpamAssassin 2.54 (1.174.2.17-2003-05-11-exp) >Subject: [BioC] change working directory command on command line >X-BeenThere: bioconductor@stat.math.ethz.ch >X-Mailman-Version: 2.1.2 >List-Id: The Bioconductor Project Mailing List <bioconductor.stat.math.ethz.ch> >List-Help: <mailto:bioconductor- request@stat.math.ethz.ch?subject="help"> >List-Post: <mailto:bioconductor@stat.math.ethz.ch> >List-Subscribe: <https: www.stat.math.ethz.ch="" mailman="" listinfo="" bioconductor="">, <mailto:bioconductor-request@stat.math.ethz.ch?subject=subscribe> >List-Archive: <https: www.stat.math.ethz.ch="" pipermail="" bioconductor=""> >List-Unsubscribe: <https: www.stat.math.ethz.ch="" mailman="" listinfo="" bioconductor="">, <mailto:bioconductor-request@stat.math.ethz.ch?subject=unsubscribe> > >Hello, > >i am trying to run Bioconductor on Unix. I am invoking >R typing R on the command line. I believe there is no >Gui available for the Unix version. It would be nice >if somebody could tell me how to change the working >directory on command line. > >Tapan Mehta > >_______________________________________________ >Bioconductor mailing list >Bioconductor@stat.math.ethz.ch >https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor Jianhua Zhang Department of Biostatistics Dana-Farber Cancer Institute 44 Binney Street Boston, MA 02115-6084
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Thank you all for the help. It would be nice if I could know about some documentation for R/bioconductor commands that can be used in Unix through command line. Thanks once again, Tapan Mehta --- John Zhang <jzhang@jimmy.harvard.edu> wrote: > If you mean changing directory from within R, then > getwd() returns the working > directory and setwd("your/working/dir") changes the > working directory to > your/working/dir. > > >Date: Fri, 6 Jun 2003 13:03:32 -0700 (PDT) > >From: Tapan Mehta <tapmehta@yahoo.com> > >To: bioconductor@stat.math.ethz.ch > >MIME-Version: 1.0 > >X-Virus-Scanned: by amavisd-milter > (http://amavis.org/) > >X-Virus-Scanned: by amavisd-milter > (http://amavis.org/) > >X-Spam-Status: No, hits=0.0 required=5.0 tests=none > version=2.54 > >X-Spam-Level: > >X-Spam-Checker-Version: SpamAssassin 2.54 > (1.174.2.17-2003-05-11-exp) > >Subject: [BioC] change working directory command on > command line > >X-BeenThere: bioconductor@stat.math.ethz.ch > >X-Mailman-Version: 2.1.2 > >List-Id: The Bioconductor Project Mailing List > <bioconductor.stat.math.ethz.ch> > >List-Help: > <mailto:bioconductor-request@stat.math.ethz.ch?subject=help> > >List-Post: <mailto:bioconductor@stat.math.ethz.ch> > >List-Subscribe: > <https: www.stat.math.ethz.ch="" mailman="" listinfo="" bioconductor="">, > > <mailto:bioconductor-request@stat.math.ethz.ch?subject=subscribe> > >List-Archive: > <https: www.stat.math.ethz.ch="" pipermail="" bioconductor=""> > >List-Unsubscribe: > <https: www.stat.math.ethz.ch="" mailman="" listinfo="" bioconductor="">, > > <mailto:bioconductor-request@stat.math.ethz.ch?subject=unsubscribe> > > > >Hello, > > > >i am trying to run Bioconductor on Unix. I am > invoking > >R typing R on the command line. I believe there is > no > >Gui available for the Unix version. It would be > nice > >if somebody could tell me how to change the working > >directory on command line. > > > >Tapan Mehta > > > >_______________________________________________ > >Bioconductor mailing list > >Bioconductor@stat.math.ethz.ch > >https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor > > Jianhua Zhang > Department of Biostatistics > Dana-Farber Cancer Institute > 44 Binney Street > Boston, MA 02115-6084 > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor
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Tapan Mehta <tapmehta@yahoo.com> [Sat, Jun 07, 2003 at 09:07:27AM CEST]: > Thank you all for the help. It would be nice if I > could know about some documentation for R/bioconductor > commands that can be used in Unix through command > line. There is no direct interface to internal R commands from any shell I know, if you mean that. You can always type echo "sqrt(2)" | R CMD BATCH and then inspect .R.Rout, which is the closest thing to what I think you mean. Greetings Johannes -- Johannes H?sing There is something fascinating about science. One gets hannes@ruhrau.de such wholesale returns of conjecture from such a trifling investment of fact. Mark Twain
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Hi all great to be part of a highly active/responsive group! Has anyone else thought about spatial correction for affy arrays? Charles Berry and I have done some simple corrections using sliding windows, see Figure 1. http://www.genome.org/cgi/content/full/13/3/513/F1 or http://naturalvariation.org/sfp/Borevitz_etal_2003_GR.pdf I know dCHIP can mask out scratches. Could there be something that would take advantage of multichip analysis, kind of like quantile normalization but that would consider the data in its original image form (rectangular matrix of feature intensities)? I often see smudges on arrays where useful data is below that needs to be locally corrected for. FYI I have the cdf package for the Arabidopsis ATH1 array here. http://natural.salk.edu/ath1121501cdf.tar.gz ## source http://natural.salk.edu/ath1121501cdf.zip ## win32 original cdf from affy http://natural.salk.edu/Ath1.cdf.zip Justin http://naturalvariation.org -----Original Message----- From: bioconductor-bounces@stat.math.ethz.ch [mailto:bioconductor-bounces@stat.math.ethz.ch] On Behalf Of Johannes H?sing Sent: Saturday, June 07, 2003 1:47 AM To: Tapan Mehta Cc: bioconductor@stat.math.ethz.ch; John Zhang Subject: Re: [BioC] Bioconductor commands in Unix online documentation request Tapan Mehta <tapmehta@yahoo.com> [Sat, Jun 07, 2003 at 09:07:27AM CEST]: > Thank you all for the help. It would be nice if I > could know about some documentation for R/bioconductor > commands that can be used in Unix through command > line. There is no direct interface to internal R commands from any shell I know, if you mean that. You can always type echo "sqrt(2)" | R CMD BATCH and then inspect .R.Rout, which is the closest thing to what I think you mean. Greetings Johannes -- Johannes H?sing There is something fascinating about science. One gets hannes@ruhrau.de such wholesale returns of conjecture from such a trifling investment of fact. Mark Twain _______________________________________________ Bioconductor mailing list Bioconductor@stat.math.ethz.ch https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor
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all robust summaries ive used: li and wong's algo, median polish and rlm within RMA appear to find these spatial artifacts as outliers (under a typical definition of an outlier). an easy way to see this is to make an image plot of the absolute value of the residuals from the model fit. On Sun, 8 Jun 2003, Justin Borevitz wrote: > Hi all great to be part of a highly active/responsive group! > > Has anyone else thought about spatial correction for affy arrays? Charles > Berry and I have done some simple corrections using sliding windows, see > Figure 1. http://www.genome.org/cgi/content/full/13/3/513/F1 or > http://naturalvariation.org/sfp/Borevitz_etal_2003_GR.pdf I know dCHIP can > mask out scratches. Could there be something that would take advantage of > multichip analysis, kind of like quantile normalization but that would > consider the data in its original image form (rectangular matrix of feature > intensities)? I often see smudges on arrays where useful data is below that > needs to be locally corrected for. > > FYI I have the cdf package for the Arabidopsis ATH1 array here. > > http://natural.salk.edu/ath1121501cdf.tar.gz ## source > http://natural.salk.edu/ath1121501cdf.zip ## win32 > > original cdf from affy > http://natural.salk.edu/Ath1.cdf.zip > > Justin > http://naturalvariation.org > > -----Original Message----- > From: bioconductor-bounces@stat.math.ethz.ch > [mailto:bioconductor-bounces@stat.math.ethz.ch] On Behalf Of Johannes Hüsing > Sent: Saturday, June 07, 2003 1:47 AM > To: Tapan Mehta > Cc: bioconductor@stat.math.ethz.ch; John Zhang > Subject: Re: [BioC] Bioconductor commands in Unix online documentation > request > > Tapan Mehta <tapmehta@yahoo.com> [Sat, Jun 07, 2003 at 09:07:27AM CEST]: > > Thank you all for the help. It would be nice if I > > could know about some documentation for R/bioconductor > > commands that can be used in Unix through command > > line. > > There is no direct interface to internal R commands from any shell I > know, if you mean that. > > You can always type > > echo "sqrt(2)" | R CMD BATCH > > and then inspect .R.Rout, which is the closest thing to what I think you > mean. > > Greetings > > > Johannes > -- > Johannes Hüsing There is something fascinating about science. One gets > hannes@ruhrau.de such wholesale returns of conjecture from such a > trifling investment of fact. Mark Twain > > _______________________________________________ > 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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On Sat, 7 Jun 2003, Tapan Mehta wrote: > Thank you all for the help. It would be nice if I > could know about some documentation for R/bioconductor > commands that can be used in Unix through command > line. www.r-project.org
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@rafael-a-irizarry-205
Last seen 9.7 years ago
?setwd On Fri, 6 Jun 2003, Tapan Mehta wrote: > Hello, > > i am trying to run Bioconductor on Unix. I am invoking > R typing R on the command line. I believe there is no > Gui available for the Unix version. It would be nice > if somebody could tell me how to change the working > directory on command line. > > Tapan Mehta > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor >
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