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
On Jul 18, 2005, at 11:08 AM, Seth Falcon wrote:
> Hi Rich,
>>
>>> 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:
>>
>> 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?!
That part worked okay for me when I used the names in the worked
example.
>
> 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
>
Thanks, Seth,
I hope that someone else cane help.;
Best wishes,
Rich
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
>
------------------------------------------------------------
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