Sean Davis <sdavis2@mail.nih.gov> writes: > You can see what the working directory is by: > > getwd() And you can see what is in the working directory with: dir()

> Sean Davis <sdavis2@mail.nih.gov> writes: >> You can see what the working directory is by: >> >> getwd() > > And you can see what is in the working directory with: > > dir() ..and (at least under RGui for Windows), you can get an interactive browser window to go on a file hunt: source(file.choose()) David Professor David Kipling Department of Pathology School of Medicine Cardiff University Heath Park Cardiff CF14 4XN Tel: +44 29 2074 4847 Fax: +44 29 2074 4276 Email: KiplingD@cardiff.ac.uk

Hi James, sean and Davis, Thanks to all of you for instant suggestions which were basically saying that I need to have the CorPlot.R file in my working directory. i must confess that I did not know this. So I went and downloaded the corPlot.R attachment available on the Bioconductor TWiki in my working directory. I still got the same error as earlier. So as suggested by david I ran the following command and got yet another error! > source(file.choose()) Error in parse(file, n, text, prompt) : syntax error on line 3 Now may be there is some thing really simple that needs to be done and I am missing it. Thanks, Swati --- "James W. MacDonald" <jmacdon@med.umich.edu> wrote: > Swati Ranade wrote: > > Hi I am trying generate scatter plots using the > > corPlot function in R and am getting the following > > error: > > > >>source("CorPlot.R") > > > > Error in file(file, "r") : unable to open > connection > > In addition: Warning message: > > cannot open file `CorPlot.R' > > This error indicates that CorPlot.R is not in your > working directory. > You can use setwd() to change the working directory > and try again. > > Best, > > Jim > > > > > > > I use the 2.0 version of R. Can any body suggest > how > > to resolve this issue? > > > > Thanks, > > > > Swati > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor@stat.math.ethz.ch > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > > -- > 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 > Stay connected, organized, and protected. Take the tour:

Hi I think Swati is trying to source the corPlot.R file so that he gets access to the corplot() function within it. Just using ... file.choose() ... doesn't achieve this, but rather returns the full path to the corPlot.R file. If he wants to both find the file *and* source it to get the corplot() function loaded in his workspace then... source(file.choose()) ...does work! I use this quite a lot because I am a dis-organised airhead who can never remember in which directory I've left a file :-) Regards David Professor David Kipling Department of Pathology, School of Medicine, Cardiff University, Heath Park Cardiff CF14 4XN Email: KiplingD@cardiff.ac.uk Tel: +44 29 2074 4847 fax: +44 29 2074 4276 >>> "James W. MacDonald" <jmacdon@med.umich.edu> 05/20/05 8:26 PM >>> Swati Ranade wrote: > Hi James, sean and Davis, > > Thanks to all of you for instant suggestions which > were basically saying that I need to have the > CorPlot.R file in my working directory. i must confess > that I did not know this. So I went and downloaded the > corPlot.R attachment available on the Bioconductor > TWiki in my working directory. I still got the same > error as earlier. So as suggested by david I ran the > following command and got yet another error! > >>source(file.choose()) I don't remember if that is what David recommended, but the actual function is file.choose(), without encapsulating in a call to source(). 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 _______________________________________________ Bioconductor mailing list Bioconductor@stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/bioconductor