[BioC] affylmGUI error when normalizing

[James Wettenhall]

Hi,

> 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

As pointed out already, R 1.9.1 is a bit old now.  It is best to use 2.0.1
(or later).  One reason why people may be posting to this list using R
1.9.1 with affylmGUI or limmaGUI is because I created an installation
bundle for Windows users with:

R + all the Tcl/Tk extensions required by limmaGUI/affylmGUI + all the
required R packages,

which some users found convenient.  Unfortunately, I haven't yet done this
for R 2.0.x.  I'm working on it, but the way I like to do it involves
building R from source (on Win32), which means that all of the required
tools (gcc, make, latex etc.) have to be working correctly.  And currently
there seems to be something wrong with my latex installation which I'm
trying to fix.  And even when things are working right, it still takes a
while to build and test thoroughly, so for now users can just grab the
limmaGUI and affylmGUI   R packages from
http://bioinf.wehi.edu.au/limmaGUI/ and
http://bioinf.wehi.edu.au/affylmGUI/ or from Bioconductor after installing
R first, rather than in a bundle.

I know there are some other affylmGUI posts I haven't responded to yet.  I
will when I have a chance...

Best wishes,
James