Experimental design determines what can be inferred from the data as well as determining the confidence that can be assigned to those inferences. Careful experimental design is essential to the successful use of microarrays.

Type of experiment

•  Two groups
 
•  Three or more groups
•  Time series 
•  Multiple conditions

The type of experiment and number of groups will affect the statistical methods used to detect differential expression.

Replicates

•  The more the better, but at least 3
•  Biological replicates better than technical

Rigorous statistical inferences cannot be made with a sample size of one. The more replicates, the stronger the inference.