MicroArray-计算系统生物与医学室.PPTVIP

Microarray Data Analysis Speaker : Hong-Chang Wang Advisor: Chuan-Yi Tang Outline Biochip DNA chip ; Gene chip Principle of Microarray Printing Hybridization Scanning Analysis Applications The challenges Biochip 目前，一般所稱的生物晶片(Biochip)廣義的來說即為將用於生物研究、檢測、治療之裝置(Devices)微小化之結果；至於其製程所使用之方法以及所使用之材料，則未必和電腦之半導體晶片類似，甚至可有全然不同之做法和用材。 DNA Chip, Gene Chip DNA Chip, Gene Chip Affymetrix- Oligonucletide array by photolithograph technology cDNA Microarray P. Brown Principle of cDNA Microarray Normalization Normalization balances red and green intensities. Imbalances can be caused by Different incorporation of dyes Different amounts of mRNA Different scanning parameters In practice, we usually need to increase the red intensity a bit to balance the green log2G-log2R plot and MA-plot 資料來源：清華大學原子科學系分子生醫光電實驗室 不同針之間的差異 不同針之間的差異 Normalization issues Within-slide Paired-slides (dye swap) Self-normalization Between slides Analysis Analysis Clustering Analysis The techniques of cluster analysis have been extensively applied to data in many fields, such as biology, medicine, psychiatry, sociology, criminology, anthropology, geology, geography, market research, economics, and engineering. Distance 1. Euclidean distance 2. Maximum (Chebychev) distance 3. Manhattan (city-block) distance 4. Pearson correlation 5. Kendall’s tau correlation 6. Spearman’s rho correlation 7. Canberra distance Pearson Correlation Clustering 的步驟 EX: 令一距離矩陣: Hierarchical clustering (Single-linkage) Hierarchical clustering (complete-linkage) Hierarchical clustering (average-linkage) Hierarchical clustering (Ward’s method) Nonhierarchical method k-Means We now consider an approach to partitioning that is usually called the k-means method. EX: Let K=2 1. 先任意的將 8 個項目分成兩個族群 : G1={A, B, C, D} ; G2={E, F, G, H} 分別計算兩個族群的中心點座標可得 = (4.25, 5.5) ; =(4.25, 4) 2. 計算各項目到兩個中心點的距離 族群 G1 : 族群 G2 : 依據距離的遠近,應將 B, D 分派到族群 G2 ;而 E, H 分派到族群 G1 ,即兩族群變為 : G1={