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

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 > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor >