[BioC] Integration

[Prasad Siddavatam]

Dear Group,

I am integrating different microarray datasets from various affymetrix, cDNA 
(single and double channel) and illumuna arrays. I have couple of questions 
regarding this analysis.

1. Do I have to treat two channel arrays as two independent 
experiments/treatments to make it to the same page as one color or affymetrix 
data?

2. What kind of normalizations (between and with arrays) I need to keep  
in mind? I was normalizing within and between arrays in an individual 
experiment and finally scale the data to zero mean and unit standard deviation. 
Is this a reasonable approach? Or do I need to do one more normalization 
between all arrays (like quantile)?

Greatly appreciate the feedback.

Prasad