[BioC] getting started

[Dennis Hazelett]

Hello,
I have been playing around with bioconductor for a few days now, trying 
to normalize data I have from genepix software. No one at my institution 
uses Bioconductor for microarray analysis (in fact, to my knowledge, 
they don't do any normalization beyond using a reference sample for one 
of the channels) so there is little help here. I have successfully been 
able to read in individual files and make nice graphs with them using 
marrayPlots, but ultimately I would like to be able to do loess, scale 
normalization between slides, and finally some sort of bayesian analysis 
for differential expression. Right now I'm stuck on reading in my data 
using marrayInput. But I don't even know that marrayInput is the best 
package--should I be using limma? I've read oh i don't know--3, 4 
vignettes?-- that each have some help on the subject of reading in data, 
but they use a data set--"swirl"--am I mistaken here or is swirl 
composed of 4 sets of microarray files that *have already been read in*? 
The widget doesn't help. Should objects like swirl correspond to 
treatment groups? Where in marrayInfo does one put information about the 
target sample? How does that get related back to actual array data? 
There's a lot of documentation on what the classes are, but not on how 
to use them. I don't expect answers to these questions--I've scoured 
vignettes and message boards for this type of info. I just want to know, 
can anyone point me in the right direction?
-Dennis