[BioC] Multifactorial affy data

[Jonathan Arthur]

Hello all,

I have a data set of the form

Gene   S1  S2   S3 .... Sn

where each column is the expression of the gene labelled by the first 
column in a different sample. The expression data come from Affymetrix 
arrays. I am new to BioConductor (and microarray analysis in general), 
so I have a few questions I hope people may be able to help me with:

1)  My expression data is the *aggregate* measure as put out by the 
Affymetrix software. The affy package appears to only deal with the 
lower level .cel files. Is there a particular reason for this? Is there 
are package capable of working with the aggregate data?

2) The various samples divide into two sets (disease and control), but 
also have clinical co-variables (e.g. male and female). I want to find 
the set of genes differentially expressed between disease and control 
while at the same time confirming those differences are specifically due 
to disease status and not to any of the other co-variables (gender, age, 
etc.)

What package(s) should I start with to do this?

Thanks in advance.

Jonathan

-- 
Dr Jonathan Arthur
Sesqui Lecturer in Bioinformatics
Central Clinical School, Faculty of Medicine and SUBIT
Medical Foundation Building, K25
University of Sydney
Ph: +61 2 9036 3132
Email: jarthur at med.usyd.edu.au