fromSaturatedSignals.SignalWeights: Weight function for scanner signals

In HenrikBengtsson/aroma: An R Object-oriented Microarray Analysis package

Description

Weight function for scanner signals.

Usage

SignalWeights$fromSaturatedSignals(x, satRatio=0.75, maxSignal=2^16 - 1, ...)

Arguments

x	A vector (or a matrix) of scanner signals for which weights are calculated.
satRatio	A double in [0,1] specifying the relative level (of the maximum signal) where saturations starts.
maxSignal	A numeric specifying the maximum scanner signal.

Details

All signals less than satRatio*maxSignal get weight one, all greater or equal to maxSignal get weight zero, and inbetween there is a linear decrease from one to zero.

Default value of argument satRatio is chosen such that saturation "starts" about 50000 for signals on the range [0,65535], which was reported by [1].

Value

Returns a vector (or a matrix) of weights in [0,1].

Missing values

Missing-value signals (NA), get zero weight.

Author(s)

Henrik Bengtsson (http://www.braju.com/R/)

References

[1] H. Lyng, A. Badiee, D.H. Svendsrud, E. Hovig, O. Myklebost, T. Stokke. Profound influence of microarray scanner characteristics on gene expression ratios: analysis and procedure for correction. BMC Genomics, 2004, 5:10.

See Also

For more information see SignalWeights..

Examples

  x <- seq(from=0, to=10^5, by=100)
  plot(x, SignalWeights$fromSaturatedSignals(x), type="l")

HenrikBengtsson/aroma documentation built on May 7, 2019, 12:56 a.m.