MGED 12: Bioconductor and R
Installation, Getting Started
Basic Introduction to R and Bioconductor. Includes information about installation and getting help. Download as pdf
Instructors
- Misha Kapushesky
- Audrey Kauffmann contact: audrey@ebi.ac.uk
- Aedin Culhane contact: aedin@jimmy.harvard.edu
Introduction
- Introduction to R and Bioconductor (powerpoint slides)
- Installing R and Bioconductor. Overview
- R Introductory Manual (please note, we have a typo in this manual the link to the R workbench should be http://wwwdev.ebi.ac.uk/Tools/rcloud
- R code
- exercise
- Samples files: ToothGrowth (text file), csv file
Additional manuals (these will not be covered in the course, but maybe helpful if you are new to R)
Quality Assessment
- R code
- E-MEXP-886 dataset
- Slides
- Quality assessment report on raw data
- Quality assessment report on normalized data
- Customized quality assessment report
EBI ArrayExpress R Workbench
Misha will present the R Workbench for analysis in R.- ArrayExpress R Workbench EBI Gene Expression Atlas
- Slides
- Gene Expression Atlas in R (PDF)
- Gene Expression Atlas in R (R code)
Exploratory Data Analysis
- Clustering and Ordination slides (powerpoint)
- Tutorial
- instructions
- R code
- rnw, if you want to build using Sweave, Stangle
If your new to R. Download R script to install packages required to run tutorial - Normalised (vsn) fibroblast data data.vsn.csv
- Samples annotation annt.txt
- Download raw data (9 cel files) as a tar.gz or a zip compressed file
- Task 4: Annotating the plots with gene information: example1.html
-
Advanced Task 1: 3D figure output.html
Course Data Files
Output from tutorial
- Worked example of hierarcical cluster analysis
- Previous Courses on Ordination, multivariate data analysis using made4. Link to Course Page
R Resources
- An excellent beginners guide to R is from Emmanuel Paradis
- Introduction to R classes and objects on R site
- Tom Short's R reference card and other contributed are useful from the R the R contributed documentation
- Stephen Eglen's publications in PLoS Computational Biology on A Quick Guide to Teaching R Programming to Computational Biology Students. It includes links to lecture notes and an overview of useful introductory books in R.
- Simple Intro to Linear Models view
Bioconductor Resources
- Bioconductor Courses
- An excellent starter to Affymetrix data analysis Jean Wu's excellent lab on Affymetrix data analysis
- Guide to importing GEO soft data files into bioconductor
- Thomas Girke's (UC Riverside) intro into R and Bioconductor
Updated. 5th Oct 2009. Aedin Culhane