[BioC] Normalize data across platforms

[Steve Taylor]

Hi,

Thanks for your reply.

> 
> Quantile normalisation is a very conservative normalisation, and there are fears in some quarters that it may lead to over-normalisation.  However, as you're comparing between datasets, this may be what you're after.
> 

I agree. I am just looking for large differences so I am hoping it might be ok.

> Alternatively, have you considered using "housekeeping" or control genes?  These should be constant across arrays, experiments etc (if you believe in them) and so could provide a good normalisation factor.
> 

Does anyone know if affy has control probes that are consistent across platforms?

Kind regards and thanks,

Steve
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Medical Sciences Division
Weatherall Institute of Molecular Medicine/Sir William Dunn School
Oxford University