[BioC] affylmGUI error when normalizing

[Aaron Hamilton]

Here is an error I get when running affylmGUI (and attempting RMA 
normalization). The errors are listed below.
I am running R 1.9.1 on a Windows XP machine. I downloaded the 
Estrogen example .cel files and the program worked fine. When I 
attempted the same with .cel files I got from the contractor who does 
our microarray experiments, there are no error messages when the raw 
data is read, but the normalization step causes a bunch of downloads 
from the net (One is  :

www.bioconductor.org/CRANrepository/repdatadesc.rda

but after that the new windows flash by too fast to read) and then 
the two error messages at the bottom of this message.

If you know anyone I should contact who might be able to troubleshoot 
these, I would appreciate it. I am a novice at R and affylmGUI.


Below is what the screen says:
__________________________________________________________________

Loading required package: limma
Loading required package: affy
Welcome to Bioconductor
         Vignettes contain introductory material.  To view,
         simply type: openVignette()
         For details on reading vignettes, see
         the openVignette help page.
Loading required package: tcltk

Warning: ActiveTcl could not be found in the Windows Registry.

Either it has not been installed or it has not been installed with 
sufficient privileges.


affylmGUI requires the Tcl/Tk extensions Tktable and BWidget which 
are not distributed with R,

but they are distributed with ActiveTcl.

To begin, type affylmGUI() or use the pull-down menu.

Searching for user-defined affylmGUI commands in 
C:/PROGRA~1/R/rw1091/library/affylmGUI/etc ...
Loading required package: reposTools
Note: You did not specify a download type.  Using a default value of: Win32
This will be fine for almost all users


Error in if ((is.null(deps)) || (length(deps) == 0) || (deps == "")) 
return(NULL) :
        missing value where TRUE/FALSE needed


Error in assign("NormalizedAffyData", NormalizedAffyData, 
affylmGUIenvironment):
Object "NormalizedAffyData" not found





-- 
Aaron Hamilton, Ph.D.
Genome Biology Division
Biosciences Directorate
Lawrence Livermore National Laboratory
7000 East Ave., L-448
Livermore, CA 94550
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