[BioC] import data for limma analysis

[Tineke Casneuf]

This question may have been asked, but I can't find the asnwer on the
mail archive. I am trying to find a way to identify differentially
expressed genes; I was recommended to use limma. I read in the manual
that I can use data analysed with other packages (like affy and others)
or that I can import data from a software program, like ArrayVision,
ImageGene, GenePix and others.

But I have Affymetrix data that are already normalised (with Affy
software); I have also calculated averages (for the replicates) and
ratios (between experiments and controls). All my data are in csv-files.
I was wondering whether I can import it from my own csv files and how to
do this (read.table() for the data and scan() for the gene names) . Or
should I import the data from the experiments and controls separatly and
then go on using the commands in the tutorial (model.matrix, c, lmFit,
makeContrasts, contrasts.fit, eBayes) or do I need to do more with my
data or maybe omit steps?

Thank you very much in advance!

--
==================================================================
Tineke Casneuf          Tel: 32 (0)9 3313692
DEPARTMENT OF PLANT SYSTEMS BIOLOGY           Fax:32 (0)9 3313809
GHENT UNIVERSITY/VIB,    Technology Park 927, B-9052 Gent, Belgium
Vlaams Interuniversitair Instituut voor Biotechnologie         VIB
e-mail:ticas at psb.ugent.be     http://www.psb.ugent.be/bioinformatics/