Notes+about+normalization

Some Normalization methods
 * LOESS
 * LOWESS
 * Affymetrix normalization methods (Phil has a NAR paper in which he covers this Affy normalization topic in depth)
 * GCRMA (introduced to me by Hojoon)
 * MAS5

paper on the topic: Comparative analysis of microarray normalization procedures: effects on reverse engineering gene networks http://bioinformatics.oxfordjournals.org/content/23/13/i282.full

Note from Phil Unless you have a certain manufacturing bias, like Affymetrix, or you know there is a predictable dye bias, like Lowess or loess, then it's usually not recommended to pre-process your data. Normalization methods can be effective if you have measured the biases, but normalization surfing usually results in wholescale altering of your data, resulting in data that now has nothing to do with your observations. I know it can be difficult to get arrays to work right, but optimizing the assay can be a better place to start. https://mail.google.com/mail/u/0/?ui=2&shva=1#inbox/137a8ea831a7d1d6

Combat Normalization @http://www.bu.edu/jlab/wp-assets/ComBat/Abstract.html

MAGE normalization