Hello,

I have a couple of questions regarding Affymetrix analysis. We have 4
> independent experiments analysing control vs test. The experiments are
> analysing different cell types with a common phenotype with the aim of
> identifying genes associated with this phenotype. The first question is - is it okay to cross compare the individual experiments with each other even though
> they were performed independently? Secondly, one of the control vs test
> experiments has been performed on the Mouse Genome 430 2.0 array, whilst the
> remaining  experiments were performed on the updated version 430A 2.0. So far,
> with the individual experiments we have been performing analysis using GCRMA on
> R, but due to the differing probe sets we can’t perform GCRMA whilst including
> the samples from the old chip version. Is there any possible way that this can
> be achieved? 

Thanks in advance


Christy 


-- 
Christy Toms D.Phil
Sir William Dunn School of Pathology
Oxford OX1 3RE
01865 285489

