I have read the manual for Robin, but I'm not certain what normalization method it uses. According to affymetrix they use Quantile normalization, but in the manual it is directly after MAS and leaves out normalisation and summarization suggesting that like MAS PLIER uses scaling normalization. I looked at the R code, but it simply says it has set normalization=T which from the documentation for R means it used quantile normalization. Which normalization method does Robin use with PLIER? Also I was wondering if PLIER applies the same Tukey bi-weight summarization method used in MAS? Thank you for any help you can provide.

Hi Martin,

in Robin, the plier will do a quantile normalization of PM and MM probes together. And you are right, plier
also uses the Tukey biweight summarization step that's used in MAS 5.0. For more details on plier please
do also refer to: http://media.affymetrix.com/support/technical/technotes/plier_technote.pdf

Best greetings,
Marc

Thanks Marc for clearing that up for me. I appreciate it.

Regards,
Martin