ECS289A
ECS 234: Microarray Data Analysis
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Lecture Slides on Microarray Data Analysis | ECS 234, Study notes of Computer Science
Material Type: Notes; Professor: Filkov; Class: Comp Functional Genomics; Subject: Engineering Computer Science; University: University of California - Davis; Term: Unknown 1989;
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Pre 2010
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ECS 234: Microarray Data Analysis
Microarray Data
Gene 6200 … … … … Gene 3 … … Gene 2 … … Gene 1 0.013 2. Plate 1 Plate 2 … Plate 10 Entries:
- Ratio of the color intensities green/red (Cy3/Cy5) (spotted) •Single color intensity (Affy)
- (^) Fishing Expeditions vs. Hypotheses: differentially expressed genes
- (^) Part/Whole Genome Hypotheses: cell/tissue classification
- (^) Gene Expression vs. Gene Function: guilt by association (co-regulation)
- (^) Transcription Regulation
- (^) Fingerprinting
- (^) Genome analysis
- (^) Gene Circuitry
What Can We Do With
Microarray Data?
- Lochart and Winzeler
Microarray Data Analysis I
- Experimental Design
- Normalization and Transformation
- Identification of differentially expressed genes
- (^) Fold test
- (^) T-test
- (^) Correction for multiple testing
- Classification
- Clustering
- Local Pattern Discovery
- Projection Methods
- (^) PCA
- (^) SVD
Microarray Data Analysis II:
Discovery
- (^) Array Design
- (^) Affy
- (^) cDNA libraries and probes
- (^) Controls
- (^) Affy: PM-MM, and others
- (^) Negative controls
- Experimental Design
(two-color DNA microarrays)
B Reference Direct (with dye swap) Loop A A R B A B A BB B AA
Lochart and Winzeler 2000
Distribution of Observed Values
Distribution of Observed Values is ~ log-normal log (Color Intensity) or log R/G is a good estimator of differential expression But one can do better by properly accounting for all systematic sources of error
- Data Acquisition and Visualization
- (^) Image quantification (spot reading)
- (^) Dynamic Range and spatial effects
- (^) Scatterplots
- (^) Systematic sources of error
1. Data Visualization
Image quantification (spot reading) Huber et al
Huber et al Spatial Effects
Checking the Data: Scatterplots
- (^) Visual Aids for Data Calibration
- (^) Plotting Red vs Green Expression Huber et al