DNA Microarray Image Analysis - University of Illinois at Urbana ...
DNA Microarray Image Analysis - University of Illinois at Urbana ... DNA Microarray Image Analysis - University of Illinois at Urbana ...
Separating Spots from Multi-Channel Imagery - Assumptions Boundary Type Statistical Assumptions Threshold Values Hyperphere Gaussian Distribution (scalar) µ + kσ dist dist Volume Uniform Distribution (1 point) V min, pts = 1 k V min,max Hyperplane Linearly Correlated Distributions (2 points) r v = ( µ ,min); µ ∈Plane,min ⊥ Plane Nonlinear Using Projections Gaussian Distribution in Projected Space (scalar) µ + kσ projected projected 62
Step 1: Separating Spots from Background - Example Original image (400x400 image size, SHORT datum type) Spot pixel counts • Hypersphere: 15913 • Volume: 509 • Hyperplane: 15877 • Nonlinear after AND operation: 13735 • Nonlinear after OR operation: 16045 63
- Page 11 and 12: 11 Microarray Data Processing Workf
- Page 13 and 14: DNA Microarray Image Analysis • T
- Page 15 and 16: Ideal Microarray Image? 1. Ideal cD
- Page 17 and 18: Microarray Image Technologies • A
- Page 19 and 20: Variations of Grid Geometry • Rot
- Page 21 and 22: Variation of Spot Morphology • Sp
- Page 23 and 24: Examples: Spatially Varying Backgro
- Page 25 and 26: 25 Examples: Spatial Resolution, Li
- Page 27 and 28: IMAGE ANALYSIS: MICROARRAY GRID ALI
- Page 29 and 30: Grid Alignment: Application Domains
- Page 31 and 32: 31 Microarray Grid Alignment: Previ
- Page 33 and 34: Microarray Grid Alignment: Previous
- Page 35 and 36: 35 Grid Alignment Algorithm Overvie
- Page 37 and 38: Image Down-Sampling • Design of r
- Page 39 and 40: Vertical and Horizontal Line Score
- Page 41 and 42: Optional Regularity Enforcement •
- Page 43 and 44: Processing Multiple Grids Line Disc
- Page 45 and 46: Spot Size & Spot Density 45 •Radi
- Page 47 and 48: Missing Spots The fewer the spots i
- Page 49 and 50: Down-sampling •Experimental resul
- Page 51 and 52: Grid Alignment Properties Color Inv
- Page 53 and 54: Multiple Grids: Semi-Automated vs.
- Page 55 and 56: 55 MICROARRAY FOREGROUND SEPARATION
- Page 57 and 58: Foreground Separation Using Spatial
- Page 59 and 60: Foreground Separation Using Intensi
- Page 61: Foreground Separation From Multi-Ch
- Page 65 and 66: Goals and Objectives of Quality Ass
- Page 67 and 68: Quality Assessment: Spot Examples
- Page 69 and 70: Criteria for Assessing Morphologica
- Page 71 and 72: I2K Selecting Valid Pixels - SNR Me
- Page 73 and 74: I2K Selecting Valid Pixels - Topolo
- Page 75 and 76: 75 MICROARRAY DATA QUANTIFICATION A
- Page 77 and 78: Spot Descriptors • Volume of fore
- Page 79 and 80: Visualization of Spot Descriptors S
- Page 81 and 82: Normalization • Normalization usi
- Page 83 and 84: 83 MICROARRAY DATA FUSION, ANALYSIS
- Page 85 and 86: Visualization • Data: 3D cubes,di
- Page 87 and 88: Web-Based Documentation 87 http://a
Step 1: Separ<strong>at</strong>ing Spots from Background - Example<br />
Original image (400x400 image size, SHORT d<strong>at</strong>um type)<br />
Spot pixel counts<br />
• Hypersphere: 15913<br />
• Volume: 509<br />
• Hyperplane: 15877<br />
• Nonlinear after AND oper<strong>at</strong>ion: 13735<br />
• Nonlinear after OR oper<strong>at</strong>ion: 16045<br />
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