Practical Statistical Analysis of DNA Microarray Data
Kolle Kolle 26-28th of October 2003
This is the homepage of a 3 day course held 26-28th of October 2003 at Kolle
Kolle, Denmark
Involved personnel:
- Vince Carey, Biostatistics, Harvard University (Lecturer)
- Sandrine Dudoit, Biostatistics, UC Berkely (Lecturer)
- Peter Dalgaard, Biostatistics, Copenhagen (Organizer)
- Kasper Daniel Hansen, Biostatistics, Copenhagen (Organizer)
- Lisbeth Carstensen, Biostatistcs, Copenhagen (Organizer)
Lecture Notes
Dudoit: Introduction to Genome Biology and Microarray Experiments
Primer on Genetics and Molecular Biology PDF
Introduction to DNA Microarray Technologies PDF
Carey: R and Bioconductor.
Slides PDF
In addition, slides prepared by Dudoit and Gentleman (for this course)
were handed out as well (only the first 40 or so pages) PDF
Dudoit: Preprocessing and Expression Measures.
Preprocessing DNA Microarray Data PDF
Software for Preprocessing DNA Microarray Data PDF
Carey: Machine Learning with Genomics Applications.
Slides PDF
Dudoit: Multiple Hypothesis Testing in Genomics.
Slides PDF
Carey: Ontology / Graph Structures I.
Slides PDF
Dudoit: Identification of Regulatory Motifs in DNA Sequences.
Slides PDF
Carey: Clustering / Graph Structurs II / Standards.
Slides PDF
Dudoit: Microarray Experimental Design and Analysis
Slides PDF
Computer Labs:
Lab 1, Concerning R, ExprSet and Annotation
PDF handout, Sweave format
Lab 2, Concerning Preprocessing af cDNA microarray data
PDF handout, Sweave format. This lab was taken from this course,
with a few modifications regarding libraries.
Lab 3, Concerning Preprocessing of Affymetrix data
PDF handout, Sweave format. This lab was taken from this course,
with a few modifications regarding libraries.
Lab 4 Concerning Machine Learning and friends
PDF handout, Sweave format.
Lab 5: End-to-End exercise
PDF handout, Sweave format.
Data, for windows users
Data, for Linux and
MacOS users
Additional Material:
Notes on Installing
R and Bioconductor (these notes are currently being rewritten to a more general
form).
Contact
K.Hansen AT THIS SERVER biostat.ku.dk