Statistics for Microarray Data Analysis Short Course, IBC2004

Gordon Smyth¹, Jean Yang², James Wettenhall¹ and Matt Ritchie¹
July 11, 2004

1. Walter and Eliza Hall Institute of Medical Research
2. Divison of Bioinformatics, University of California, San Francisco

WEHI

Course Outline

• outline.pdf

Lecture Slides in PDF format

• http://bioinf.wehi.edu.au/marray/ibc2004/lectPDF.html

Lab Exercises

Each lab description lists the required software and data for that lab. An overall list of software for the entire workshop is given in the following section (Required Software).

1. Lab 1. lab1.html lab1.pdf
   • Reading raw two-color microarray data into R, comparing the performance of different image analysis software using diagnostic plots, identifying control spots and blank spots on the arrays, and normalizing the data.
2. Lab 2. lab2.html lab2.pdf
   • Reading raw Affymetrix microarray data into R, assessing the quality of the data using diagnostic plots, and normalizing the data.
3. Lab 3. lab3.html lab3.pdf
   • Fitting linear models to microarray data, finding differentially expressed genes, linking gene lists to external databases, using diagnostic plots to assess the performance of the linear model, and using Venn diagrams to find genes differentially expressed for more than one pair of conditions.
4. Lab 4. lab4.html IBCLab4.pdf IBCLab4.R
   • Classification and clustering of microarray data.

Required Software

• http://bioinf.wehi.edu.au/marray/ibc2004/Required/

As well as checking the overall list of required software, you may also wish to check each individual lab sheet for a list of software required for that lab.

Required Data

Please check whether you already have the Estrogen package from the Required Software.

• maDataIBCnoEstrogen.zip
• maDataIBCwithEstrogenWin32.zip (for Windows)
• maDataIBCwithEstrogenSource.zip (For Unix/Linux/MacOS X)

• Cell line comparison Data (12.1Mb)
• Swirl Zebrafish Data (2.4Mb)
• ApoAI Knockout Data (1.2Mb)
• Estrogen Data (as an R package) (36.3Mb)
• EstrogenTargets.txt

Past Microarary Workshops

• Singapore Statistical Methods in Microarrays - IMS
• DSC 2003 Bioconductor Workshop (provides an introduction to genome biology)
• Bioconductor short courses list