[BioC] number of affy-chips needed to fit rma model

[Rafael A. Irizarry]

from my experience 2 is enough. there may be some issues but, IMHO, it
will certainly be better than using mas 5.


On Mon, 12 Jul 2004, Dipl.-Ing. Johannes Rainer wrote:

> hi to all,
> 
> i'm in a lab where we made our first affymetrix chips, and now i want to do some
> normalization steps to correct for the errors. i'm not really convinced about
> the method that affymetrix provides (mas 5) so i read now many papers about how
> to normalize affymetrix chips. the method i like is the rma method from
> irizarry, but i do not know if we have enough chips to fit the model parameters
> well. by now we have only 2 chips, one with a treatment, the other without. does
> anybody know how many chips i need to fit models like rma or vsn well into the
> data?
> other question, how do i know what's the best method to normalize my data?
> 
> thanks, jo
> 
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