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微陣列資料之群集分析 (Clustering Analyses on Microarray Data)

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介紹透過群集計算分析微陣列資料。

日期 : 2015/05/07

Introduce clustering analyses on microarray data. Furthermore, use GAP (Generalized Association Plots) software to introduce the general flow of analyzing microarray data.

Date : 05/07/2015

Published in: Science
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微陣列資料之群集分析 (Clustering Analyses on Microarray Data)

  1. 1. Bioinformatics • Date: 2015/05/07 (Thu.) • Jian-Kai Wang, GSB`s MD r02b48005@ntu.edu.tw http://jiankaiwang.no-ip.biz/ Clustering analyses on microarray data (w/ Chapter 9, Bioinformatics and Functional Genomics, 2nd )
  2. 2. Content 2 1 Introduction .1 implement microarray data analysis .2 Generalized Association Plots (GAP) 2 Start analyzing (download java, GAP first link) .1 Data preparation .2 Clustering analyzing 3 Result 4 Accomplishment .1 Modifying parameters
  3. 3. 1.1 implement microarray data analysis 3 introduction Visualized Software Generalized Association Plots (GAP) Biometric Research Branch-ArrayTools (BRB-ArrayTools) … Programming Package in R Significance Analysis of Microarrays (SAM) Linear Models of Microarray Data (limma) … • Continue the context, while implementing microarray data analysis
  4. 4. 1.2 Generalized Association Plots (GAP) • Developed by the group leaded by Chun-Houh Chen, research fellow, Institute of Statistical Science, Academia Sinica (more) • A Java-based software • Website: http://gap.stat.sinica.edu.tw/Software/GAP/ • Aim: generalized association plots and exploratory data analysis in omics data, including microarray data 4 introduction
  5. 5. 2.0 Prepare the execution environment • Install Java SE Development Kit 8 Downloads – Verify Java version: http://www.java.com/en/download/installed.jsp – First 2 columns: from official website – Last 2 columns: from lab website 5 analyzing STEP 1 STEP 2
  6. 6. 2.0 Prepare the execution - GAP • Install GAP v.0.2.7.d – First 2 columns: from official website – Last 2 columns: from lab website 6 analyzing Back
  7. 7. 2.1 Data preparation – know input data 7 analyzing Gene names Samples NA na null (blank) CellCycle_20150503.txt additional (how to remove ?)
  8. 8. 2.2 Clustering analyzing – working area 8 analyzing Data/result View Analyzing menu Color legend Chart selection (mouse tools) Main GAP window Control panelResponding bar Output messages
  9. 9. 2.2 Clustering analyzing – import data 9 analyzing Yd Yc Xd Xc
  10. 10. 2.2 Clustering analyzing – view the data 10 analyzing multiple data selection viewport
  11. 11. 2.2 Clustering analyzing – start analyzing 11 analyzing STEP 1 STEP 2 (data type) STEP 3 (dimensions) STEP 4 (methods)
  12. 12. 2.2 Clustering analyzing – analyzing result 12 analyzing Column Proximity Matrix Row Proximity Matrix More detailed information Sample names Gene names
  13. 13. 2.2 Clustering analyzing – start clustering 13 analyzing STEP 1 STEP 2 STEP 3 Clustering result Both average-linkage
  14. 14. 3.1 Modifying parameters – color legend 14 result Change target Change Color legend
  15. 15. 4 Accomplishment - export 15 result Output path The path you installed the GAP
  16. 16. 4 Accomplishment - export 16 result Path in Chinese is not allowed
  17. 17. Exercise 17 exercise Source The same one with the tutorial with all data Row clustering method Centroid-linkage Column clustering method Single-linkage Color legend To Raw Data Matrix with (Red, Blue, Yellow) bar
  18. 18. End 18 ending • feel free to contact me r02b48005@ntu.edu.tw http://jiankaiwang.no-ip.biz/

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