Summary
Objectives:
Microarray gene expression experiments have a complex technical background. Knowledge
about certain technical details is inevitable to judge alternatives for both experimental
design and analysis. Here, we introduce the necessary details for the so-called two-color
microarray experiments and review major sources of technical variance.
Methods:
We follow the sequence of experimental steps during a typical two-color microarray
gene expression experiment, stressing decisive points in the choice of technique,
experimental handling and biophysical basics. We point out where technical variation
is to be expected.
Results:
Tissue storage, RNA extraction techniques, as well as the microarray hybridization
represent major components of technical variance to be considered. Depending on the
possibilities for access to the biomedical material under investigation, choice of
amplification and labeling techniques can also be decisive to avoid additional technical
variance. The two-color microarray experimental approach seeks to avoid a group of
probe-level technical biases making use of the advantages of an incomplete block-design.
Conclusions:
It is worth to know the major sources of technical variance during the typical experimental
sequence, both for choice of experimental design and techniques of molecular biology,
as well as for the understanding of quality control and normalization approaches.
Here, early investments pay at the level of reduced technical variance, allowing for
enhanced detection levels for the effects under investigation.
Keywords
Agilent - chip - comparative hybridization - gene expression - microarray - technical
variance
