Normalization of microarrays can be achieved by a variety
of methods. Initially, normalization may include subtraction
of local background intensity values. These background
values are taken from the quantification data files.
The normalization methods included with Iobion GeneTraffic
software can be applied on either the global or the
sub-array level. Global normalization is performed on
the array as a whole and each qualified spot is included
in the calculation. Sub-array normalization is performed
on qualified spots in the individual print-tip groups
(grids, sub-arrays, blocks) in order to account for
systematic differences caused by the movements of the
arraying robot and for surface defects on the printed
slide.
GeneTraffic offers the
following normalization methods:
- Raw Intensity
- Log2 Ratio
- Reference Genes
- Housekeeping Genes
- LOWESS (Locally Weighted
Scatter Plot Smoother)
- Custom Value
