estimateParameter {CALIB} | R Documentation |
Estimate the calibration model parameters according to the known concentration and the measured intensities of external control spikes on each array.
estimateParameter(spike, RG, bc = FALSE, area = TRUE, errormodel = "M")
spike |
a SpikeList object. |
RG |
a RGList_CALIB object. |
bc |
a logical value. TRUE means background corrected measured
intensities are used. Default is FALSE . |
area |
a logical value. 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 . |
errormodel |
a character to indicate the distribution of spot capacity. "A" means spot capacity is additive. "M" means spot capacity is multiplicative. Default is "M". |
This function estimates calibration model parameters. In this function,
the model parameters are estimated separately for each microarray,
based on the measured intensities of the external control spikes and
their known concentration in the hybridization solution. It accepts
spike measured intensities and concentration from 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.
An ParameterList
object containing the components:
MuS |
matrix containing MuS for each array. |
Ka |
matrix containing Ka for each array. |
P1 |
matrix containing P1 of each dye for each array. |
P2 |
matrix containing P2 of each dye for each array. |
SigmaA |
matrix containing sigma additive for each array. |
SigmaM |
matrix containing sigma multiplicative for each array. |
SigmaS |
matrix containing sigma spoterror for each array. |
SpotError |
matrix containing the spot error of each spot for each array. |
Method |
boolean values indicating the way to calculate the measured intensities. |
ErrorModel |
character "M" or "A" to indicate the type of spot
capacity distribution. |
Hui Zhao
Engelen, K., Naudts, B., DeMoor, B., Marchal, K. (2006) A calibration method for estimating absolute expression levels from microarray data. Bioinformatics 22: 1251-1258.
# 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)