Bioconductor short course
A short course on
Computational and Statistical
Aspects of Microarray Analysis
Kitasato University
July 14-25, 2003
Lecturer:
Robert
Gentleman
Schedule of Topics
| Monday, July 14 | Tuesday, July 15 | Wednesday, July 16 | Thursday, July 17 | Friday, July 18 | |
| Lecture | Introduction to Genome Biology | R/S Programming Techniques | DNA Microarray Data, Oligonucleotide Arrays | Introduction to Bioconductor | Experimental Design and Experimental Design Paper |
| Labs | Lecture Con't | Lab1, Lab2a | Lab2b | Lab3b | Estrogen |
| Monday, July 21 | Tuesday, July 22 | Wednesday, July 23 | Thursday, July 24 | Friday, July 25 | |
| Lecture | Holiday, No Lecture | Microarray Experiments and Distances and Expression Measures | Some Things Every Biologist Should Know About Machine Learning | Classification in Microarray Experiments | Clustering in Microarray Experiments |
| Labs | Holiday | Lab4 | Lab5 | Lab6, Lab7 | Lab8 |
Lab materials
| Lab1 | Bioconductor Basics | |||
| Lab2a | Bioinformatics (anotation package) | |||
| Lab2b | An Introduction to Some Graphics in Bioconductor | |||
| Lab3a | Introduction to Bioconductor's marray Packages | |||
| Lab3b | Introduction to the affy package | |||
| Lab4 | Differential Gene Expression | |||
| Lab5 | Cluster Analysis Using R and Bioconductor | |||
| Lab6 | Classification Using R and Bioconductor | |||
| Lab7 | Analyzing Microarray Data: From Images to List of Candidate Genes | |||
| Lab8 | Application of Machine Learning to Microarray Data, SVM and friends |
Milan 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(tkWidgets)
library(Milan)
vExplorer()
and select the package Milan and the vignette for a given lab,
e.g., lab1.Rnw.
Installing software
The packages used for this course require the use of R version 1.7.1 or newer.
A download script has
been provided. To use, type
'source("/workshops/Milan/getMilan.R")' in your R session
and then 'getMilan()'. There are a few arguments to
getMilan(), tho most users will not find them necessary:
- getAllDeps: If this is TRUE, will automatically attempt to download any package dependencies, otherwise the user will be prompted. Default is TRUE.
- destdir: This defines where to install the packages. Defaults to .libPaths()[1]
- force: If TRUE, will install a package even if not all of its dependencies were available. Default is TRUE.
- versForce: If TRUE, will install a binary package even if it was built on a different version of R. Default is TRUE.
- method: The download method to use, same as in download.packages(). Default is 'auto'.
Alternatively, you can download the individual packages
here:
- affy: Source, Win32
- affydata: Source, Win32
- Annotate: Source, Win32
- Biobase: Source, Win32
- bioclabs: Source, Win32
- cluster: Source, Win32
- DynDoc: Source, Win32
- e1071: Source, Win32
- edd: Source, Win32
- ellipse: Source, Win32
- genefilter: Source, Win32
- geneplotter: Source, Win32
- GO: Source, Win32
- golubEsets: Source, Win32
- hgu95av2: Source, Win32
- hu6800: Source, Win32
- KEGG: Source, Win32
- mAffyu95a: Source
- marrayNorm: Source, Win32
- Milan: Source, Win32
- multtest: Source, Win32
- randomForest: Source, Win32
- tkWidgets: Source, Win32
Documentation
Main R
website: R manuals, R News.
Main Bioconductor website:
Bioconductor short course, vignettes, talks,
publications.