文档介绍：Affymetrix GeneChip Data Analysis?Chip concepts and array design?Improving intensity estimation from probe pairs level ?Clustering?Motif discovering and preliminary resultHow is Affymetrix Gene Chip made?Affymetrix Gene Chip Procedure?Target preparation Isolate mRNA ?cDNA ?cRNA? 35~200 base fragments?Target Hybridization:200?l cocktail? probe array chip ? hybridization (16 hours at 40~60°C)?Washing and Staining?Probe array scan, Data analysis, and Interpretationbiotinylatedfragmented(12-15ug)Concepts of Array DesignPM to maximize hybridization MMto ascertain the degree of cross-hybridizationPMMMProbe setProbe pairSignal Intensity Estimation?Absolute analysisaverage difference ?(PM-MM) / pairs parison analysisexperimental subtract baseline average difference?Probe pairs variationprobe pairs outlier (cross-hybridization)arraysoutlier (image contamination)?Probe pairs level adjustmentWing Wong Lab dChip: least square fitting model built from multiple chips Affymetrix MAS : imputation Clustering?Affymetrix DMTexamine the SOM, are the clusters tight ? experiment primarily with "Number of Epochs", "Alpha_i" and "Sigma_i" parameters to reduce error. multiple level clustering examine filtering parameters to adjust min and max value. (default is 20 and 20000)?Wing H. Wong Lab dChipfrom image file to outlier detection and clustering ?MIT