R/maanova - Tutorials

Differential Expression In Factorial Design

Tutorial demonstrating how to test for differential expression using microarray data in a factorial design. This self-guided tutorial includes all the necessary data files. An R script contains step-by-step explanations of the analysis. After uncompressing, please see the README.txt file for instructions.

DE_tutorial.zip
README.txt

For more information about the experimental samples:

Chromosome Y variants from different inbred mouse strains are linked to differences in the morphologic and molecular responses of cardiac cells to postpubertal testosterone
Llamas B, Verdugo RA, Churchill GA, Deschepper CF.
BMC Genomics. 2009 Apr 7;10:150. PMCID: PMC2679052 [ Full Text ]

For more information about the analysis of these data:

Importance of randomization in microarray experimental designs with Illumina platforms
Verdugo RA, Deschepper CF, Muñoz G, Pomp D, Churchill GA.
Nucleic Acids Res. 2009 Sep;37(17):5610-8. PMCID: PMC2761262. [ Full Text ]

To speed up the tutorial, only the first 3000 of the probes in the microarray are included. The full dataset is available at the GEO database, record GSE15354.

Here are some graphics generated by the tutorial: