[BioC] Please help: AffylmGUI errors (more detail)

[Aaron Hamilton]

Hello, here are some more details on how I got the errors below:
I am running AffylmGUI with the latest version of R (2.0.1) on a Windows XP
machine. As far as I can tell I have all the packages and activeTcl 
re-installed,
although perhaps something is missing?
I have .cel files for affymetrix data, just simple comparisons (a control vs. a
manipulated cell sample), which I load into AffylmGUI. The step where 
I load the
raw data (select targets file) seems to work OK, and now do does the 
RMA normalization step. I can
get the chart (normalized intensity box plot) of the normalized data 
and it looks OK. But when I get to the 'Linear model: compute 
contrasts' step and beyond, I get the error messages at the bottom.

Here is the transcript from the R window

>  library(affylmGUI)
Loading required package: limma
Loading required package: tcltk
Loading required package: affy
Loading required package: Biobase
Loading required package: tools
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: reposTools

ActiveTcl was found in the Windows Registry (for LOCAL_MACHINE), installed in
C:\Tcl
This directory will be added to the Tcl search path to enable affylmGUI
to find the Tktable and BWidget extensions.

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

Searching for user-defined affylmGUI commands in 
C:/PROGRA~1/R/rw2001/library/affylmGUI/etc ...
Background correcting
Normalizing
Calculating Expression
Loading required package: tkrplot
Note: You did not specify a download type.  Using a default value of: Win32
This will be fine for almost all users

[1] "Attempting to download hgu133a from 
http://www.bioconductor.org/data/metaData/"
[1] "Download complete."
[1] "Installing hgu133a"
[1] "Installation complete"
Loading required package: hgu133a
[here I attempted to get the M-A plot anyway, and it was abnormal]





Errors from linear model/compute contrasts step

Error in inherits (x,"data.frame"):subscript out of bounds
Error in assign ("fit", fit, affylmGUIenvironment):Object "fit" not found

Error in get(x,envir,mode,inherits):variable "fit" was not found
(Then window to pick contrasts)
Error in NCOL(fit$coefficients):object "fit" not found
Error in min(contrastsFit$df):object "contrastsFit" not found
Error in try(expr,TRUE):Object"ebayesAvailable" not found




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-- 
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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