[BioC] spike-dependent microarray normalization

[Barbara Cegielska]

Dear R-Users,

I use home-made spotted arrays to do some research contected with 
alergies. The matrix consist of : 60% of the genes are up-regulated and 
40% of genes that are down-regulated and spikes. I didn't use any genes 
with constant expression. How I should analyse this experiment?  
According to statistics I should focuse on external spike  controls and 
compare all genes with spikes. It is two coulour experiment.  So I have 
to build quite complicated statistical model.  I'm not sure if it is a 
right pathway. What do you think?

Regards,

Barbara