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 ...
Normalization • The motivation for normalizing microarray images and/or extracted descriptors comes from the fact that one would like to compare results obtained from multiple slides, scanners, or laboratories, and with multiple microarray techniques. The difficulty of performing meaningful comparisons arises from different slide preparations (e.g., amounts of mRNA), scanner settings, microarray protocols or labeling specifics. • The purpose of normalization is to adjust for these variations, primarily for label efficiency and hybridization efficiency, so that we can discover true biological variations as defined by the microarray experimental studies. 80
Normalization • Normalization using Statistical Descriptors — Z-Transformation I NORM STAT Z −TRANSFORM ( row, col) = Irowcol ( , ) − µ σ — Background Correction des ⎛ X − X ⎞ = ⎜ ⎟ ⎝ ⎠ CHANNEL 0 CHANNEL 0 X WRT BKG FRG BKG LOG RATIO log 2 CHANNEL1 CHANNEL1 XFRG − XBKG 81
- 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 and 76: 75 MICROARRAY DATA QUANTIFICATION A
- Page 77 and 78: Spot Descriptors • Volume of fore
- Page 79: Visualization of Spot Descriptors S
- 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
Normaliz<strong>at</strong>ion<br />
• The motiv<strong>at</strong>ion for normalizing microarray images and/or<br />
extracted descriptors comes from the fact th<strong>at</strong> one would<br />
like to compare results obtained from multiple slides,<br />
scanners, or labor<strong>at</strong>ories, and with multiple microarray<br />
techniques. The difficulty <strong>of</strong> performing meaningful<br />
comparisons arises from different slide prepar<strong>at</strong>ions (e.g.,<br />
amounts <strong>of</strong> mRNA), scanner settings, microarray protocols<br />
or labeling specifics.<br />
• The purpose <strong>of</strong> normaliz<strong>at</strong>ion is to adjust for these<br />
vari<strong>at</strong>ions, primarily for label efficiency and hybridiz<strong>at</strong>ion<br />
efficiency, so th<strong>at</strong> we can discover true biological vari<strong>at</strong>ions<br />
as defined by the microarray experimental studies.<br />
80
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