Hinrich Gohlmann & Willem Talloen 
Gene Expression Studies Using Affymetrix Microarrays [PDF ebook] 

The Affymetrix Gene Chip system is one of the most widely adapted microarray platforms. However, due to the overwhelming amount of information available, many Affymetrix users tend to stick to the default analysis settings and may end up drawing sub-optimal conclusions. Written by a molecular biologist and a biostatistician with a combined decade of