ABSTRACT
Abstract ....................................................................................................................20 Introduction ..............................................................................................................20 Methods ................................................................................................................... 21
Statistical Principle of Normalization .......................................................... 21 Little Differentiation Versus Substantial Differentiation .............................23 Differentiation Fraction and Undifferentiated Probe Set .............................24 Spatial Pattern and Subarrays .......................................................................24 Linear Approximation and Its Applicability ................................................24 High Breakdown Estimation and Simple Least Trimmed Squares ..............25 Symmetric and Trimmed Solutions of Simple Linear Regression ...............26 Multiple Arrays and Reference .....................................................................26 Statistical Breakdown of Normalization ......................................................26
Examples and Results ..............................................................................................27 Implementation and SUB-SUB Normalization ............................................27 Parameter Selection ......................................................................................27 Variation Reduction by Subarray Normalization .........................................27 Usage of Mismatch Probes ...........................................................................28 Affymetrix Spike-in Data Set .......................................................................29 Perturbed Spike-in Data Set ......................................................................... 32 Comparative Functional Genomics and Primate Brain Expression
