[BioC] Microarray data analysis for experiments using amplified RNA

[Swati Ranade]

Hi,
I have done some experiments using amplified RNA (Rayan Baugh's method which
I modified slightly) probes with affy chips. The study design is a simple
comparison of knockout mutant vs wild type. My question was: Is it ok to use
the same statistical algorithms one would apply for standard microarray
experiments or do I need to follow a different strategy? Can anybody give
pointers?

Thanks,

Swati

Swati Ranade
Bauer Center for Genomics Research
7 Divinity Av
Cambridge 
MA 02138