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 ...
µσ Spot Screening Quality Criteria: GenePix and QuantArray Inspection Criteria Description SNR for each channel Signal and background variability Excessively high background µ /( µ + µ ); m /( m + m ) k sig sig bkg sig sig bkg * µ / σ ; k * µ / σ sig sig sig bkg bkg bkg µ Global /( µ Global + µ ); m Global /( m Global + m ) bkg bkg bkg bkg bkg bkg Saturation − count 1 saturated count all Proportion of signal above µ+k*σ of background Spot Shape Foreground and background uniformity count > k* σ count 4π A Perim 2 all ; if µ > µ + kσ then count + 1 sig bkg bkg > k* σ ( Isig ,max − Isig ,min ) ( Ibkg ,max − Ibkg ,min ) 1 − ;1− Range Range 70
I2K Selecting Valid Pixels – SNR Method • SNR is computed directly from mean of background and foreground pixels • SNR criterion eliminates spots with — no signal (SNR~1), — very weak signal (1
- 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 and 68: Quality Assessment: Spot Examples
- Page 69: Criteria for Assessing Morphologica
- 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
I2K Selecting Valid Pixels – SNR Method<br />
• SNR is computed directly from mean <strong>of</strong> background and<br />
foreground pixels<br />
• SNR criterion elimin<strong>at</strong>es spots with<br />
— no signal (SNR~1),<br />
— very weak signal (1
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