The AgilentFilterRG node in SciCraft has the
following input arguments:
- RG: Raw microarray data in the form of a RG limma
object, [1], of unnormalised untransformed
intensities. (As produced by the AgilentLoad and gprload nodes)
- BothChannels: Logical. If TRUE, both channels in a spot
must be too weak/saturated for the spot to be removed.
- NotFound: Text box specifying how spots that are not found are to be
handled. Has the following two alternatives:
- Remove spots that are not found (default)
- Ignore spotfinding
- ControlSpots: Text box specifying how control spots are to be
handled. Has the following three alternatives:
- Weigh down controls (default)
- Remove controls
- Keep Control spots
- FilterMethod: Text box specifying how filtering is done. Has the
following four alternatives:
- Remove spots (default)
- No filtering
- Reduce spot weight to
.
- Reduce spot weight to
.
- NoiseWeights: Text box specifying what type of weights that are
going to be used for each spot based on its estimated
uncertainty(s). Has the following three choices:
- No noise weights (default)
- Weigh by
- Weigh by
- RedMinIntensity: Float with the minimum intensity in the red
channel for a gene to be kept for further analysis.
- GreenMinIntensity: Float with the minimum intensity in the green
channel for a gene to be kept for further analysis.
- RedBgRatio: Float specifying the minimum ratio of red foreground to
background.
- GreenBgRatio: Float specifying the minimum ratio of green foreground to
background.
- SaturationLimit: Integer specifying the maximum number of
saturated pixels allowed.
- PixelLimit: Float specifying the number of foreground pixels.
- MaxMDev: Float specifying the maximum spot uncertainty.
The output arguments from the node are:
- RGfiltered: RG limma object [1], with the filtered, untransformed
microarray data.
Bjørn Kåre Alsberg
2006-04-06