Dye bias appear from the fact that the two dyes used, Cy and Cy
,
have slightly different physical properties, and the react slightly
different to photo-bleaching, an effect that occurs in multiple
scannings of the array, [2]. Environmental factors such as the
level of ozone, is also a contributing factor.
According to [2], a rule of thumb during normalisation should be to normalise all local features first, and then gradually progress to normalisation that involves several arrays. It is also recommended to correct for spatial effects before normalising for dye effects, since the dye and spatial effects can be confounded [2, page 133]. In SciCraft you can use the two nodes NormWithinArrays and NormBetweenArrays. The first concentrates on normalising within the arrays (local features), and the second one normalises between arrays (global features).
The NormBetweenArrays normalises expression values to achieve consistency between arrays. Normalisation between arrays is usually, but not necessarily, applied after normalisation within arrays (NormWithinArrays node).
Bjørn Kåre Alsberg 2006-04-06