Statistical Algorithms Description Document Genechip ® Array Design Data Outputs Stat Pairs Used

OVERVIEW This document is a detailed reference guide for the Statistical Algorithms used in the analysis of GeneChip ® expression data. The guide focuses on how they work, what calculations and approaches they comprise, and how the tunable parameters are designed. Additional references are provided for additional information. It is important to understand how a GeneChip ® array is designed when considering the most appropriate approaches for its analysis. A GeneChip ® probe array cons ists of a number of probe cells where each probe cell contains a unique probe. Probes are tiled in probe pairs as a Perfect Match (PM) and a Mismatch (MM). The sequence for PM and MM are the same, except for a change to the Watson-Crick complement in the middle of the MM probe sequence. A probe set consists of a series of probe pairs and represents an expressed transcript. The statistical algorithms provide the following data outputs: Output Descriptions Signal A measure of the abundance of a transcript. The number of probe pairs in the probe set. The number of probe pairs in the probe set used in the Detection call.