[BioC] Error messages in affylmGUI on PC with respect to plotting

Richard Friedman friedman at cancercenter.columbia.edu
Fri Jul 15 20:25:48 CEST 2005

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"
 [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:


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

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



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


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

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.

Richard A. Friedman, PhD
Associate Research Scientist
Herbert Irving Comprehensive Cancer Center
Oncoinformatics Core
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

" 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

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