DNA Microarray Image Analysis - University of Illinois at Urbana ...

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Data Quantification • Data quantification (or spot feature extraction) refers to extracting descriptive values of foreground and background pixels for each spot. • Ideally, extracted descriptors (also called features or attributes) should be directly proportional to the mRNA quantity in the solution that was deposited in a spot, and should represent the deposited gene expression level. • In reality, fluorescent intensity measurements in each channel might be scaled or distorted differently according to some linear or non-linear functions during data preparation steps. 76
Spot Descriptors • Volume of foreground intensity FRG Volume = ( µ − µ )* A FRG BKG FRG • Logarithmic ratio des X RATIO = X X CHANNEL 0 FRG CHANNEL1 FRG des ⎛ X − X ⎞ = ⎜ ⎟ ⎝ ⎠ CHANNEL 0 CHANNEL 0 X WRT BKG FRG BKG LOG RATIO log 2 CHANNEL1 CHANNEL1 XFRG − XBKG • Regression Ratios 77
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February 4, 2005 DNA Microarray Ima
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Publications • Journals: — Bajc
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Microarray Problem: Major Objective
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Input and Output of Microarray Data
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Types of Expected Microarray Data M
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11 Microarray Data Processing Workf
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DNA Microarray Image Analysis • T
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Ideal Microarray Image? 1. Ideal cD
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Microarray Image Technologies • A
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Variations of Grid Geometry • Rot
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Variation of Spot Morphology • Sp
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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 and 62: Foreground Separation From Multi-Ch
Page 63 and 64: Step 1: Separating Spots from Backg
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: 75 MICROARRAY DATA QUANTIFICATION A
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
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DNA Microarray Image Analysis - University of Illinois at Urbana ...

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