estimateParameter(spike, RG, bc = FALSE, area = TRUE, errormodel = "M")SpikeList object.RGList_CALIB object.TRUE means background corrected measured
intensities are used. Default is FALSE.TRUE means spot area is used to calculate
measured intensities. Namly, measured intensities are calculated by
foreground intensities(or background corrected intensities, if bc is
TRUE ) multiply spot area. FALSE means spot area is not used.
Default is TRUE .ParameterList object containing the components:"M" or "A" to indicate the type of spot
capacity distribution.spike argument,
which is an object of SpikeList class. It supports different ways to calculate the measured intensities.
Arguments bc and area are logical and their combinations is used
for specifying four differents ways. bc indicates using background correction
or not. area indicates multiplying spot area or not. The default value
of these two arguments are bc = FALSE and area = TRUE.
The argument errormodel is to specify the distribution of spot capacity
of each array. The spot capacity is either additive or multiplicative.
Whichever distribution is more appropriate will depend largely on the type of
microarray slide and spotting procedure used. The spot parameters mus and sigmas
can be considered equal for all measurements of a single array.
The argument RG is for calculating the maximum intensity of each array. These
maximum intensities are used to estimate the upper saturation level of each array.
More details please refer to the reference literature.
# load data: RG and spike
data(RG)
data(spike)
# for the measured itensities, take the default bc=FALSE and area=TRUE.
# use multiplicative spot error model
parameter <- estimateParameter(spike,RG)
Run the code above in your browser using DataLab