Analysing yeast time course microarray data
This page contains links, updated R code, and other information relating to the paper
Gillespie, C. S., Lei, G., Boys, R. J., Greenall, A. J., Wilkinson, D. J.,
2010. Analysing yeast
time course microarray data using BioConductor: a case study using yeast2
Affymetrix arrays BMC Research Notes, 3:81. 
Since this paper contains a lot of R code that can go out of date, I have set up this page to fix any issues that may crop up.
Documents
Initially these documents will be the same as the above paper. However, overtime they will gradually diverge.
- Analysing yeast time course microarray (pdf).
- Code: Main paper. Additional functions: ExtractIDs.R, RemoveProbes.R.
- Pombe and Cerevisiae Filter
- Or you can download it from the Affy website - requires a free Affymetrix user account.
- Yeast Annotation File
- Or you can download it from the Affy website - requires a free Affymetrix user account.
Updates/Corrections since publication
- (11/06/2010) Paper updated to reflect the new array express download format. Thanks to Saeed Salem for pointing this out.
Suggestions, bugs, queries
If you have any questions or queries about the above material, then feel free to contact me at c.gillespie@ncl.ac.uk Also if you think of any other techniques that could be included in the paper, then please send in your suggestions.
R Courses
I am running four R courses in September 2012:
- Course 1: Introduction to R. This course assumes no prior knowledge of R, programming or statistics.
- Course 2: Statistical modelling with R. A one day course on statistical modelling techniques.
- Course 3: Programming with R. This course is a follow-on from the introduction to R course.
- Course 4: Advanced graphics with R.
See the course web site for further details.