The FilterRG node in SciCraft is used in the process of removing, or down-weighting,
noisy spots or arrays from the
data set. There are several quality measures that can be used when deciding
if a spot or an array should be kept out of, or down-weighted throughout the analysis:
- Amount of saturated pixels,
- Spot size/shape
- Mean-median correlation
- Spot-related coefficient of variation,
- Foreground/Background-ratio (F/B-ratio)
- Signal to noise ratio,
- Level of heterogeneity of background
- Irregularities of spot size,
- Variability in local background,
- Score level of local background,
- Composite quality score,
The desired procedure is to give weights to the different
spots, depending on the flag value they are give in the image analysis
process. In practice 'bad' spots are given less weight and 'good'
spots more weight. The R package limma, gives you the option of
defining your own weight functions, depending on how strict you
are. Typically, spots removed are given weights equal, or very close to zero.
Subsections
Bjørn Kåre Alsberg
2006-04-06