Short Course

A short course on
Computational and Statistical Aspects of Microarray Analysis

Bressanone, Italy
June 7th-11th, 2004

Lecturers:
Robert Gentleman
and
Wolfgang Huber

Schedule of Topics

	Monday, June 7	Tuesday, June 8	Wednesday, June 9	Thursday, June 10	Friday, June 11
Lecture 1	Programming in R, S Programming Techniques, Recent Developments in R and S Graphics	Quality Control and Further Topics on Preprocessing and Solving the Riddle of Bright Mismatches	Differential Expression, Univariable Screening by ROC Curve Analysis, Differential Gene Expression, Testing for Differential Expression and Differential Expression with the Bioconductor Project	Unsupervised Learning Methods For Analysis of Microarray Data and Exploratory Data Analysis for Microarray Data	Networks in Molecular Biology and Graph, RBGL and Rgraphviz
Lecture 2	Error Models and Normalization	Annotation in Bioconductor and Using GO	Combining Experiments	Machine Learning and Classification in DNA Microarray Experiments	Graphs, EDA, and Computational Biology and High Throughput Protein-Protein Interaction Data
Lab	Using R and Bioconductor	Preprocessing and Quality Control	Annotation and meta-data	Machine Learning	Introductory Graph Lab
Packages Used		arrayMagic, estrogen and lymphoma	ALL, GOstats, graph, RBGL and Rgraphviz

Lab materials

Lab1	Using R and Bioconductor	.pdf	.Rnw	.R
Lab2	Preprocessing and Quality Control	.pdf	.Rnw
Lab3	Annotation and meta-data	.pdf	.Rnw	.R
Lab4	Machine Learning	.pdf	.Rnw	.R
Lab5	Introductor Graph Lab	.pdf	.Rnw	.R

Installing software

For notes on software installation, follow the "HowTo" link on the Bioconductor website. The following software should be installed for the Bressanone course.

From CRAN: R version 1.9.0 (Linux, Windows, MacOS).
From Bioconductor
- All Bioconductor packages from release 1.4, using the install script: getBioc(libName="all").
- Annotation data packages: hgu95av2, hgu133a, GO.
- Experimental data packages: ALL, estrogen, lymphoma.

Documentation

Official Course Website
Main R website: R manuals, R News.
Main Bioconductor website: Bioconductor short course, vignettes, talks, publications.

bioconductor.org

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