This website provides a set of software tools to quantitate,
process, and combine data from a set of experiments performed with a
two-color DNA microarray. DNA microarrays provide an extremely
powerful method for comparing mRNA abundances in one cell population
relative to another and are now used pervasively throughout the
molecular biology and genomics communities (background and more
information may be found
here or at gene-chips.com).
These tools are arranged in a pipeline. Starting with a set
of scanned microarray images, tools may be invoked consecutively to
ultimately produce an expression matrix, listing the mRNA
ratio for each gene (matrix rows) in each experiment (matrix columns).
Also provided is a statistic lambda for each gene and
experiment, reflecting how likely it is that the gene is expressed
differently between the two cell populations compared.
These tools are most useful when two or more replicate microarray
experiments are available, providing two or more samples of
expression (per gene per condition). In fact, lambda values are calculated
only if replicate samples are available. In our own
laboratory, we typically perform all experiments in quadruplicate (at the least),
generating four microarray images per pair of conditions compared.