CLASS SCHEDULE and READING LIST, SPRING 2002
A detail from Paul Cézanne's "Pommes et biscuits"
1879-1882, from the Musée de l'Orangerie, Paris.
Cézanne was a precursor of expressionism in more ways than it
is sometimes realized....
A detail from Paul Cézanne's "Pommes et biscuits"
1879-1882, from the Musée de l'Orangerie, Paris.
Cézanne was a precursor of expressionism in more ways than it
is sometimes realized....
| March
25 OVERVIEW OF THE COURSE
Discussion of the logistics of the class, exam policy, software suggestions, overview of the schedule. Open discussion on additional topics that should be covered. Gene Expression, Speed T Wald Lecture 2001 presentation materials Nature Genetics Special Issue: the Chipping Forecast Microarray Data Analysis J Quackenbush presentation materials Introduction to genome biology and DNA
microarray experiments
Gentlemen R Dudoit S presentation
materials
March 27 cDNA
ARRAY TECHNOLOGY (Qin Bin Guo, JHU)
Overview of the basic biological principles behind gene expression microarray measurements and the steps involved in carrying out a gene expression experiment. A Concise Guide
to cDNA Microarray Analysis
Expression profiling
using cDNA microarrays.
April 1 OLIGONUCLEOTIDE
ARRAYS MODEL--BASED EXPRESSION INDICES (Rafael
Irizarry, JHU)
Overview of the data structures associated with oligonucleotide arrays, and procedures for normalization and quality control. Comparison of methods for the derivation of expression indices from probe--level data. It includes the Li--Wong method implemented in D-chip, the approaches used in the Affymetrix software and the library affy in R Model-based analysis
of oligonucleotide arrays: Expression index computation and outlier detection
Exploration, Normalization,
and Summaries of High Density Oligonucleotide Array Probe Level Data.
GeneLogic workshop
on Low-Level analysis of Affymetrix GeneChip data Presentation
materials
April 3 NORMALIZATION
Overview of methods and software for the normalization of microarray data. cDNA microarray experiments: preprocessing and experimental design Gentlemen R Dudoit S presentation materials Ratio-based decisions
and the quantitative analysis of cDNA micro-array images
Normalization
for cDNA Microarray Data
SNOMAD software Standardization and Normalization of Microarray data. Tutorial
on
the Loess curve--fitting approach.
April 8
MORE ON NORMALIZATION AND THE NEED FOR REPLICATION
Illustration of sma library for normalization. Discussion of reproducibility of microarray experiments and its implication for the design and interpretation of array experiments. SMA
R library Normalization of Microarray data, and more.
Importance of
replication in microarray gene expression studies: Statistical methods
and evidence from repetitive cDNA hybridizations
April 10 IDENTIFYING
GENES THAT ARE DIFFERENTIALLY EXPRESSED ACROSS TWO TISSUE TYPES
Discussion of approaches for establishing whether genes that are differentially expressed across two samples or two groups of samples. Development of
a prostate cDNA microarray and statistical gene expression analysis package
Significance
Analysis of Microarrays
Determining Significant
Fold Differences in Gene Expression Analysis
April 15 MULTILEVEL
MODELING OF MICROARRAY DATA
Introduction to multilevel modeling for describing the variabiilty of gene expression ratios across the genome. On differential
variability of expression ratios: Improving statistical inference about
gene expression changes from microarray data.
Microarrays,
Empirical Bayes Methods, and False Discovery Rates.
A Bayesian framework
for the analysis of microarray expression data: regularized t-test and
statistical inference of gene changes.
Cyber-T
Bayesian analysis of two-group Microarray data.
April 17 SAMPLE
SIZE
Approaches for determining the number of replications in the design of microarray experiments. April 22 ANALYSIS
OF VARIANCE MODELS FOR MICROARRAYS
Using principles of DOE (design of experiments) to improve microarray analyses. Design and Analysis
of Gene Expression Microarray Experiments
April 24
VISUALIZATION OF MICROARRAY DATA
Approaches to the visualization of gene expression patterns, including basic hierarchical clustering and dendrogram construction. Cluster analysis
and display of genome-wide expression patterns
The transcriptional
program in the response of human fibroblasts to serum.
Computational
analysis of microarray data. Quackenbush, J
Clustering in
an Object-Oriented Environment
Examples
of cluster Analysis in R.
Peter Rousseeuw,
Anja Struyf and Mia Hubert
Apr 29 PRINCIPAL
COMPONENT ANALYSIS
Tutorial on Principal
Components Analysis Link
May 1 BINARY
CLASSIFICATION
A Tutorial on
Logistic Regression
Stat
Soft documentation and tutorial on discriminant analysis.
Classification
Flexible discriminant
analysis by optimal scoring
Data Mining Class
Notes
Machine Learning
of Rules and Trees
May 6 COMPARISON
OF CLASSIFIERS
Methods of Comparison
for classifiers
Comparison of
Discrimination Methods for the Classification of Tumors Using Gene Expression
Data
May 8 CASE
STUDIES IN MOLECULAR CLASSIFICATION OF CANCER: I
Molecular Classification
of Cutaneous Malignant Melanoma by Gene Expression Profiling.
May 13 CASE
STUDIES IN MOLECULAR CLASSIFICATION OF CANCER: II
Diversity of gene expression in adenocarcinoma
of the lung
AutoClass
Unsupervised classification
May 15 INTRODUCTION
TO BIOCONDUCTOR MICROARRAY LIBRARIES IN R
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