Analyzing DNA Microarray Data Using Bioconductor
Sandrine Dudoit and Robert Gentleman
Fred Hutchinson Cancer Research Center
December 4-6, 2002
Fred Hutchinson Cancer Research Center
December 4-6, 2002
Wednesday, December 4th
AM
Outline (Slides in pdf)
Introduction to Genome Biology (Slides in pdf)
Introduction to DNA Microarray Technologies (Slides in pdf)
PM
Pre-processing DNA Microarray Data (Slides in pdf)
LAB: R and Bioconductor Basics (Slides in pdf,SeattleR package: Lab1.Rnw)
Thursday, December 5th
AM
Using Bioconductor Packages (Slides in pdf)
LAB: Using Bioconductor Packages (SeattleR package: Lab1.Rnw)
PM
LAB: Bioconductor Packages for Pre-processing DNA Microarray Data (SeattleR package: Lab4a.Rnw, Lab4b.Rnw)
Only one PM session
Friday, December 6th
AM
Distances (Slides in pdf), Cluster Analysis (Slides in pdf)
LAB: Distances, Cluster Analysis (SeattleR package: Lab3.Rnw)
PM
Feature Selection, Classification
LAB: Feature Selection, Classification (SeattleR package: Lab5.Rnw)
R packages for the short
course
Seattle: (Linux/Unix) (Windows)
golubEsets: (Linux/Unix) (Windows) (Golub et al. (1999) ALL AML microarray dataset)You can go through the labs using the function vExplorer from the tkWidgets package. At the R prompt type
library(tkWidgets)and select the package
library(Seattle)
vExplorer()Seattleand the vignette for a given lab, e.g., Lab1.Rnw.You may also need to download the
ellipseande1071packages from CRAN, and thehu6800data package from the Bioconductor data package section.General documentation for R and Bioconductor can be found in the "Documentation" section of the Bioconductor website (links under "Documentation" in the left side bar).
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