Hi Rich, On 15 Jul 2005, friedman at cancercenter.columbia.edu wrote: > I have installed affylmGUI on a PC and upon opening it got > the > error message By "upon opening" do you mean you typed: library("affylmGUI") The more detailed you can be, the better our chances of being able to help. > Error message: Error in eval(expr,envir,enclos):Object "plot > Options" not found. > > Upon using the Estrogen Test set and trying to display the Intensity > Density Plot I got the following error messages: Again, you need to show us exactly what you entered (along with the error message). > > Error in FUN(newX[,i],...): wromg type for argument 2 is called > massdist > > and > > Error in title(PlotTitle): Plot new has not been called yet. > > As far as I know, i have installed everything asked for correctly. > (affylmGUI, TclTK, Limma, Tkrplot, affyPLM, R2HTML, and Xtable(. After loading the affylmGUI package, run the sessionInfo() function and report its output in a followup post. That will tell us your version of R along with the versions of the attached packages. + seth

Seth and everybody, On Fri, 15 Jul 2005, Seth Falcon wrote: > Hi Rich, > > > By "upon opening" do you mean you typed: > > library("affylmGUI") > When I typed the above command, nothing happened. When I pulled down affylmGUI command from the R pull down menu (it had been previously loaded) I got the error message Error message: Error in eval(expr,envir,enclos):Object "plot Options" not found. The associated screen message when I got this is > local({pkg <- select.list(sort(.packages(all.available = TRUE))) + if(nchar(pkg)) library(pkg, character.only=TRUE)}) > affylmGUI() Searching for user-defined affylmGUI commands in C:/PROGRA~1/R/rw2010/library/affylmGUI/etc ... The results of the sessionInfo command was: > sessionInfo() R version 2.1.0, 2005-04-18, i386-pc-mingw32 attached base packages: [1] "splines" "tcltk" "tools" "methods" "stats" "graphics" [7] "grDevices" "utils" "datasets" "base" other attached packages: hgu95av2probe hgu95av2cdf R2HTML xtable tkrplot "1.1" "1.5.1" "1.54" "1.2-5" "0.0-12" affydata affyPLM gcrma matchprobes affylmGUI "1.4.1" "1.3.3" "1.1.4" "1.0.22" "1.2.7" limma affy reposTools Biobase "2.0.2" "1.6.7" "1.5.19" "1.5.12" > The more detailed you can be, the better our chances of being able to > help. > I then followed the affylmGUI worked example: File->New I got a box that said "Choose working directory" I chose the directory which contained my files. I clicked "okay" I got a box that said: "Please select a tab-delimited file listing the CEL files. No filename is selected at the moment. Press the Select Targets File Button." I did and got a list of files. I clicked "estrogen" (I can send the file as an attachement if that might help). I got a box that read "Targets File C:\Program Files\R\rw2010\library\estrogen\extdata\estrogen.txt I clicked "OK" on that box I got a box that said "Data Set Name Please eneter a name for this data set " I clicked entered Estrogen and clicked "OK" The title on the status window now reads "Estrogen" instead of "untitled" I clicked on Raw Affy Data and it said available. I clciked on Normalized Affy Data and Linear Model Fit, and both said "unavailable'. I clicked on RNATargets and table containing the target file was displayed. It corresponded to what I had read in. I closed the table >From the plot menu, I chose "Intensity Density Plot" A box appeared that said: Please Sepcify: Choose a slide. I chose "Abs10.1" and clicked "OK". I got a menu that read Probe set PM probes MM probes Both I left it at "PM Probes and clicked OK". It said Plot Title: PM Intensity distribution for Abs 10.1 X axis Label: log2(PM Intensity) Y Axis Label: Density I left it as is And clicked OK. I got an error message Error in approx(xords,kords,x): need at least two non-NA values to interpolate. I clicked OK Then I got an error message that said Error in title(plotTitle): plot.new has not been called yet. I clicked OK. I did not see PM Intensity display as in the affylmGUI worked example. I hope that this is sufficient detail to let someone who reads this figure out what is worng. I greatly appreciate the help. Thanks and best wishes. Rich ------------------------------------------------------------ Richard A. Friedman, PhD Associate Research Scientist Herbert Irving Comprehensive Cancer Center Oncoinformatics Core Lecturer Department of Biomedical Informatics Box 95, Room 130BB or P&S 1-420C Columbia University Medical Center 630 W. 168th St. New York, NY 10032 (212)305-6901 (5-6901) (voice) friedman at cancercenter.columbia.edu http://cancercenter.columbia.edu/~friedman/ " I know what is going to happen next in 'Middlemarch'. Mr. Featherstone left Fred his money, and the lady who wants his money is going to tell everybody that Fred gambles and it is going to be in all the papers in Middlemarch." Rose Friedman, age 8

Hi Rich, On 15 Jul 2005, friedman at cancercenter.columbia.edu wrote: >> library("affylmGUI") >> > > When I typed the above command, nothing happened. > When I pulled down affylmGUI command from the R pull down menu > (it had been previously loaded) I got the error message > > > Error message: Error in eval(expr,envir,enclos):Object "plot > Options" not found. > > The associated screen message when I got this is > >> local({pkg <- select.list(sort(.packages(all.available = TRUE))) > + if(nchar(pkg)) library(pkg, character.only=TRUE)}) >> affylmGUI() I see the same error here. This is something for the package maintainer to address. > The results of the sessionInfo command was: Looks like you have recent versions of things. > I then followed the affylmGUI worked example: > > File->New > > I got a box that said > > "Choose working directory" > > > I chose the directory which contained my files. > > I clicked "okay" > > I got a box that said: > > "Please select a tab-delimited file listing the CEL files. > > No filename is selected at the moment. Press the Select Targets File > Button." > > I did and got a list of files. > > > I clicked "estrogen" (I can send the file as an attachement if > that might help). > > > I got a box that read > > "Targets File > > C:\Program Files\R\rw2010\library\estrogen\extdata\estrogen.txt > > I clicked "OK" on that box I tried this same thing and see an error message that estrogen.txt is not the correct format as it does not contain a FileName header or some such. I tried modifying the headers in estrogen.txt but even with FileName as a header, I still received the same error message?! I'm not sure what to suggest at this point other than contacting the package maintainer. The detail you've provided should be enough for someone more familiar with the affylmGUI package to help sort things out. Best, + seth