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experimental design
home information experimental design: variation

It is important to try and develop a model that effectively deals with the many sources of variance that can be introduced. With a microarray experiment, there are four major contributors to variance:

The genes or probes which are spotted:

  • Each probe spotted on the array may differ in length or GC content thus affecting the hybridisation efficiency and kinetics
  • Each corresponding cDNA or cRNA that is labelled and hybridised to the array will differ in length, labelling efficiency and abundance

The arrays themselves:
  • Each array is made separately even if it was made in a single batch and thus may exhibit differences in spot quality
  • Each array is printed onto a separate piece of glass or silicon
  • Often times, a project may utilise arrays from multiple batches/lots

The dyes being used:
  • Each of the dyes used differ in photostability, brightness, detectability and incorporation efficiency
  • A large experiment may require use of dyes from different batches/lots

The treatments involved:
  • Each treatment is performed individually and will have its own effects
  • Treatments may be done at different times
  • Treatments may even be done by different people