The FilterRG node in SciCraft has the
following input arguments:
- FilterInfo: Additional raw data used for
filtering. E.g information concerning saturation of spots.
- RG: RG limma object of unnormalised
untransformed intensities. That is objects produced by the
AgilentLoad and gprload nodes.
- GeneStatus: String specifying the status of the genes. E.g
``gene'' (default) or ``cDNA''.
- BothChannels: Logical, if TRUE then both channels in a spot must
be too weak/saturated for the spot to be removed.
- Flags: Text box indicating how flagged spots are to be
handled. Has the following three options:
- Remove spots with negative flags (default)
- Keep flagged spots
- Reduce spot weight to
.
- ControlSpots: Text box specifying how control spots are
handled. Has the following three options:
- Weigh down controls (default)
- Remove controls
- Keep Control spots
- FilterMethod: Text box specifying how the filtering is done. Has
the following five options:
- Remove spots (default)
- No filtering
- Reduce spot weight to 0
- Reduce spot weight to
.
- Reduce spot weight to
.
- NoiseWeights: Text box specifying how to compute weights for each
spot based on its estimated uncertainty(ies). Has the following
three options:
- No noise weights (default)
- Weigh by
.
- Weigh by
- RedMinIntensity: Float specifying the minimum intensity in the
red channel for a gene to be kept for further analysis. Default set
to
.
- GreenMinIntensity: Float specifying the minimum intensity in the
green channel for a gene to be kept for further analysis. Default set
to
.
- RedBgRatio: Float specifying the minimum ratio of red foreground
to background. Default set to
.
- GreenBgRatio: Float specifying the minimum ratio of green foreground
to background. Default set to
.
- SaturationLimit: Integer specifying the maximum proportion of
saturated pixels that is permitted in percent. Default value is
.
- PixelLimit: Float specifying the minimum number of foreground
pixels, Default value is
.
- MaxMDev: Float specifying the maximum spot uncertainty. Default
value is
.
- delta (
): Float specifying the fudge factor for noise
weights. (I.e used to compute noise weights.
The output arguments from the node are:
- RGfiltered: RG object containing the filtered
untransformed microarray data. That is, objects having the same form as objects produced by the
AgilentLoad and gprload nodes.
Bjørn Kåre Alsberg
2006-04-06