Design of microarray experiments

For meaningful comparisons of multiple microarray experiments the initial overall design of the experiments is crucial. This includes the necessary controls, replicates etc. Even simple questions may demand 8 to 16 microarray experiments performed from individual biological samples that were processed in parallel. Some examples from the reference cited below are shown here. An example of a typical large microarray study that would be performed for researchers of the SFB is shown here. Data from an original experiment are shown here: pdf (68kB), xls (104kB).

Literature

Yang YH, Speed T. Design issues for cDNA microarray experiments. Nat Rev Genet. 2002 Aug;3(8):579-88


Selection of an appropriate design for high density microarray experiments

Examples for the most common microarray designs realized in conjunction with Agilent 4x44k microarrays are shown here.