EMBO 2003
The Bioconductor Project:
Open-source Statistical Software for the
Analysis of Microarray
Data
Sandrine Dudoit
Division of Biostatistics,
University of California, Berkeley
EMBO Practical Course on Analysis and Informatics
of Microarray Data
Wellcome Trust Genome Campus, Hinxton
Cambridge, UK
March 18, 2003
Lecture notes
Overview of Bioconductor software, annotation, pre-processing:
.pdf
Supplement on differential gene expression, clustering,
classification: .pdf
Lab materials
| Lab1 | R and Bioconductor Basics | |||
| Lab2 | Introduction to Bioconductor Annotation Packages | |||
| Lab3 | Introduction to Bioconductor marray Packages | |||
| Lab4 | Introduction to Bioconductor affy Package |
EMBO03 course package (Linux/Unix) (Windows).
You can step through the labs interactively using the vExplorer
function and GUI from the tkWidgets package. At the R prompt
type
library(EMBO03)
vExplorer()
and select the package EMBO03 and the vignette for a given lab,
e.g., lab1Basics.Rnw.
Installing software
For notes on software installation, follow the "HowTo" link on the Bioconductor website. The following software should be installed for the EMBO03 course.
- From CRAN: R version 1.6.2 (Linux, Windows, MacOS).
- From Bioconductor
-
- All Bioconductor packages from release 1.1.
Use install script: getBioc(libName="all", isDevel=FALSE).- Annotation data packages: hu6800, hgu95a, GO.
- Data package for Golub et al. (1999) ALL AML microarray study: golubEsets (developmental).
- EMBO03 course package (Linux/Unix) (Windows).
Documentation
Main R
website: R manuals, R News.
Main Bioconductor website:
Bioconductor short course, vignettes, talks,
publications.