Hi Ozge, I would recommend you to have a look at the simpleaffy package from Crispin J Miller. http://bioconductor.org/packages/1.9/bioc/html/simpleaffy.html The vignette pdf explain how to extract genes significantly regulated when you have replicate in you experiment. David --- David RUAU Institute for Biomedical Engineering -Cell Biology- Universitatsklinikum Aachen, RWTH Pauwelsstrasse 30 52074 Aachen GERMANY On Feb 28, 2007, at 2:10 PM, Ozge Gursoy-Yuzugulu wrote: > Hello, > > I am working on 2 isogenic cell lines which are treated with a > certain chemical and 24h, 48h, and 72 hour samples are taken. We now > have 12 arrays (4x 3 time points) and its duplicate. I searched for > some methods for the analysis of this kind of data, yet I could not > find one. > > Could you please advise me the most convenient R package and > statistical method to perform such an analysis... > > Thank you all, > > Ozge >