[BioC] Beginner: resources, WebArray and CARMAweb.

[Paolo Innocenti]

Hi all,
I'm a new PhD student: I will work on gene expression in Drosophila 
(using Affymetrix GeneChip 2.0), but before running the arrays I would 
like to learn how to analyze them.
After successfully installing R and the BioConductor packages, I have 
some problems in finding the right packages for my purposes.

My questions:

- A good place to begin with? I found these links:
	http://www.bioconductor.org/docs/
	http://www.bioconductor.org/pub/docs/mogr/

- Where can I find raw data (the concept of raw data is still unclear in 
my mind) in the right format (the concept of right format is still 
unclear as well) to improve my skills in R and to test the packages?

- I found a few web-based applications for "friendly" microarray 
data-analysis, using R and BioConductor packages (e.g. WebArray or 
CARMAweb): are they a good substitute for the command-line (at least 
during the apprenticeship), widespread-used?

Thanks,
kind regards,
Paolo Innocenti

PS. More details: I work on sex-dependent gene expression in D. 
melanogaster, looking for sexual conflict in different loci, so I will 
(roughly) make a comparison between expression of genes in high- and 
low-fitness male, high- and low-fitness female, and the offspring.