Design of microarray experiments (no date) [incomplete]
There are a variety of research designs that you can use in a microarray experiment.
Designs for cDNA arrays
Loop designs [explain]
A dye swap design use the treated DNA as red on the first array and as green on the second array. The control is green on the first array and red on the second. A second pair of treated and control DNA would use a third and fourth array.
In contrast, a loop design has overlap between pairs of treated and control DNA. It still uses the first treated DNA sample as red on the first array and green on the second. The first control uses red on the second array and green on the third. The second treated DNA sample is red on the third array and green on the fourth. This continues similarly. The last control DNA sample is red on the last array and green on the first array. The return to the last sample to the first array is the loop design.
Expression level polymorphism is a quantitative variation in gene expression associated with a complex process such as resistance.
Duplicate samples give the biggest boost in power. Triplicates and higher levels of replication provide smaller but still significant gains.
Designs for Affy arrays
This work is licensed under a Creative Commons Attribution 3.0 United States License. It was written by Steve Simon.