[BioC] affycoretools question

[Louisa A Rispoli/AS/EXP/UTIA]

Hi all-

I am fairly new to bioconductor and am very excited about the example
described in the affycoretools vignette since 1) it would make my mentor
very happy (almost the exact situation that we have in the data set), 2)
seemed like a simple solution to a issue I was not sure how to approach and
3) package seemed straightforward and easy to use.  This is probably a
stupid question arising from the fact that I have yet to fully understand R
and bioconductor but I have tried to spend a better portion of the day
trying to figure where I am going wrong and having no luck. I am trying to
compare samples (two treatment groups)  amplified two different ways and
see which differentially expressed genes are shared between the two
different methodologies. According to the PCA plot I need to compute the
expression values for each methodology separately and then combine the
data. I can not seem to create the new expression set properly to perform
the limma analysis.   I have attached a text file with my R code.

 If anyone could point me in the right direction (either the mistake I am
makeing or even the vignette that I should read closer) I would appreciate
the help. Sorry if this seems very silly but we do not have anyone here
familiar with Bioconductor to go to for help.

Thanks

Louisa

(See attached file: affycoretoolsJune232008.txt)

"If we knew what we were doing, it wouldn't be called Research." - Albert
Einstein

Louisa Rispoli, Ph.D. Reproductive Physiology
Department of Animal Science
University of Tennessee, Knoxville
A105 Johnson Animal Research and Teaching Unit
1750 Alcoa Highway
Knoxville, TN 37920
phone:(865) 946-1874
fax:(865) 946-1010
email: lrispoli at utk.edu