Software
- QTL mapping
- Gene expression
- Genome Browser
This is a multiple factor 28-array experiment. This experiment was done in Beverly Paigen's lab in The Jackson Lab. They took three strains of mice and feed them with two kind of diets. In that way you get six kind of mice. They picked two individuals in each group then you have totally 12 distinct mice. So in this experiment, you have strain, diet and biological replicates as the factors. You can test the effects from any factor or any combination of them. The experimental deign is shown below. The mice used in the experiment are:
| Hi Fat diet | Low Fat diet | |
| Strain: Pera | A1, A2 | E1, E2 |
| Strain: I | B1, B2 | F1, F2 |
| Strain: DBA | C1, C2 | D1, D2 |
The array assignment is:
There are 31,200 spots on each array so the analysis of the whole data set is very time consuming. We hand picked 300 genes to speed up the calculation. The data were picked after data normalization (joint lowess) so there are no data quality check and normalization steps in the script.
Click the following links to download the data file, design file and the script:
