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 ...
Criteria for Assessing Background and Foreground Intensities • Background intensity variations • Foreground and background intensity uniformity q STAT FRG • Foreground intensity saturation • Signal-to-noise ratio q µ GLOBAL GLOBAL LOC& GLOB 1 BKG LOC& GLOB 2 BKG BKG = ; q LOCAL GLOBAL BKG = LOCAL GLOBAL µ BKG + µ BKG mBKG + mBKG σ FRG ABS = 1− ,max ,min ,max ,min 1 I FRG − I FRG ABS BKG BKG FRG ; BKG 1 I − q = − q = − I µ Range q FRG CONT SATURATION count = 1− saturated count m ( ) ( ) Range all q CATEG SATURATION = 1; if count < T % saturated 0; if count ≥T % saturated MEAN MEDIAN q = µ /( µ + µ ); q = m /( m + m ) SNR FRG FRG BKG SNR FRG FRG BKG 68
Criteria for Assessing Morphological Properties of Foreground • Spot shape — Area-based q A −A A− A = ; q = exp( − ) AREA1 0 AREA2 0 SHAPE SHAPE A0 A0 — Perimeter-based q AREA3 SHAPE = A− A A 0 *100% q PERIM SHAPE = 4π A C 2 — Diameter-based q L−L L−L = ; q = exp( − ) X−SECTION1 0 X−SECTION2 0 SHAPE SHAPE L0 L0 • Spot location (spot displacement or position offset) — Distance-based 69
- 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 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: Quality Assessment: Spot Examples
- 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
Criteria for Assessing Morphological Properties <strong>of</strong> Foreground<br />
• Spot shape<br />
— Area-based<br />
q<br />
A −A A−<br />
A<br />
= ; q = exp( − )<br />
AREA1 0 AREA2<br />
0<br />
SHAPE<br />
SHAPE<br />
A0 A0<br />
— Perimeter-based<br />
q<br />
AREA3<br />
SHAPE<br />
=<br />
A−<br />
A<br />
A<br />
0<br />
*100%<br />
q<br />
PERIM<br />
SHAPE<br />
= 4π<br />
A<br />
C<br />
2<br />
— Diameter-based<br />
q<br />
L−L L−L<br />
= ; q = exp( − )<br />
X−SECTION1 0 X−SECTION2<br />
0<br />
SHAPE<br />
SHAPE<br />
L0 L0<br />
• Spot loc<strong>at</strong>ion (spot displacement or position <strong>of</strong>fset)<br />
— Distance-based<br />
69
Change language