[BioC] affy troubles

[peter robinson]

Dear Bioconductors,

I would like to use the affy and multtest packages to extract a list of 
differentially expressed genes from a set of 8 experiments, in which 4 are 
wildtype and 4 are knockouts. I have worked through several of the affymetric 
vignettes and the mult test vignette, which are all very well done. However, 
for some reason, I cannot extract a proper n x m matrix with n= probe sets 
and m = samples.
My steps:

library(affy)
Data<-ReadAffy()   /* Loads 8 .cel files with no error message  */
eset <- rma(Data   /* also OK   */
ex <- exprs(eset)  

I would like to get a matrix object similar to "golub" from the Vignette. 
However, there are several differences. Firstly, "ex" has labels for the 
probe_ids for all genes and does not display as a 12488 x 8 matrix (the 
output of dim(ex), but rather as a (12488x8) x 2 matrix in which the first 
column is the probe id and the second column is the expression level. Also, 
there is no separate attribute such as golub.gnames.

Several of the downstream analyses as described in the multtest vignette do 
not work properly, but I assume that the main problem is here.

Any ideas?

Thanks

Peter