Bioconductor Class
The Bioconductor Project:
Open-source Statistical Software for the
Analysis of Microarray
Data
Katherine S.
Pollard
Division of Biostatistics,
University of California, Berkeley
QB3
Microarray Course
University of California, Santa Cruz
August 15, 2003
Class notes
Full overview of Bioconductor software: .pdf
Lecture slides: .pdf
Lab materials
| Lab1 | R and Bioconductor Basics | ||
| Lab2 | Introduction to Bioconductor Annotation Packages | ||
| Lab3 | Introduction to Bioconductor marray Packages |
UCSC03 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(UCSC03)
vExplorer()
and select the package UCSC03 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 UCSC03 course.
- From CRAN: R version 1.7.1 (Linux, Windows, MacOS).
- From Bioconductor
-
- All Bioconductor packages from release 1.2.
Use install script: getBioc(libName="all", isDevel=FALSE).- Annotation data packages: hu6800, hgu95av2, GO.
- Data package for Golub et al. (1999) ALL AML microarray study: golubEsets (developmental).
- UCSC03 course package (Linux/Unix) (Windows).
Documentation
Main R
website: R manuals, R News.
Main Bioconductor website:
Bioconductor short course, vignettes, talks,
publications.