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Bioconductor is an open source and open development software project
for the analysis and comprehension of genomic data.

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Analyzing DNA Microarray Data

Analyzing DNA Microarray Data Using Bioconductor
Robert Gentleman
DSC 2003, Vienna, Austria
March 19, 2003



AM

Introduction to Genome Biology
Introduction to DNA Microarray Technologies Slides

PM

Distances
Cluster Analysis

LAB: Distances, Cluster Analysis (Seattle R package: Lab3.Rnw)
LAB: Feature Selection, Classification (Seattle R package: Lab5.Rnw)



R packages for the short course

unix/linux win
golubEsets click click Golub et al. (1999) ALL AML microarray dataset
Hu 6800 annotation click click
HGU95A annotation click click
Gene Ontologies click click
KEGG click click Kyoto Encyclopedia of Genes and Genomes
Seattle click click
Estrogen click click
VIntro click click
CRAN click click for the e1071, ellipse and randomForest packages

You can go through the labs using the function vExplorer from the tkWidgets package. At the R prompt type

library(tkWidgets)
library(Seattle)
vExplorer()

and select the package Seattle and the vignette for a given lab, e.g., Lab1.Rnw. 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).

© Copyright 2003, All rights reserved


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