Rintro

A 1 day R introductory course for non-programmers, using microarrays as main thread. Also includes an intro to Bioconductor and the eSet infrastructure. Initially set up for the diXa Microarray Analysis using R and Bioconductor training (see tags for specific courses). Partially based on the Beginners guide to solving biological problems in R (see also here) course by Robert Stojnić, Rob Foy, John Davey, Laurent Gatto and Ian Roberts.

Slides

The slides provide a general introduction to R and the main data structures. Scripting and plotting is presented by means of exercises using microarray data as example. Finally, Bioconductor and the microarray eSet/ExpressionSet classes are introduced and compared to the previous introductory material and exercises.

Exercises

1. Using R interactively and running a script.
2. Vectors
3. How to store microarray data
   • expression data and meta data
   • matrices, data frames and lists.
4. A short microarray analysis
   • reading spreadsheets into R
   • saving/loading objects
   • basic plotting
   • for loops: counting differentially expressed genes in three microarray result data
5. Another microarray analysis
   • combining multiple expression matrices and produce a heatmap
   • extracting, parsing and visualising genes of interest
6. A short Bioconductor data analysis
   • Quality control
   • Exploratory data analysis

See also

See the TeachingMaterial repository for more material.

This material is licensed under the Creative Commons Attribution-ShareAlike 3.0 License.