adjustP2: Adjust model parameter P2

In CALIB: Calibration model for estimating absolute expression levels from microarray data

Description

Adjust the calibration model parameter P2 according to the measured intensities of all clones spotted on the array.

Usage

adjustP2(RG, parameter, arrayindex = arrayindex, colorindex = colorindex)

Arguments

RG	an RGList object.
parameter	a ParameterList object.
arrayindex	integer vector specifying the index of the arrays of whose the parameter P2 needed to be adjusted.
colorindex	integer vector specifying which color needed to be adjusted.

Details

RG is an RGList_CALIB object which contains all the experimental data. parameter is the return result of function estimateParameter. arrayindex is an integer vector. It gives the index of the arrays whose P2 is needed to be adjusted. colorindex is an integer vector. It gives the color needed to be adjusted. 1 means red P2 and 2 means green P2.

Value

It returns a ParameterList object with a adjusted P2 compared to the input argument parameter.

Note

The user should decide on which array and which color the adjustment is needed. Therefore it is important to specify the right array index and color index. There is no check on this in the function.

Author(s)

Hui Zhao

Examples

# load data: RG and parameter:
data(RG)
data(parameter)

# adjust P2
parameter_new <- adjustP2(RG,parameter,arrayindex=c(1,2),colorindex=c(2,2))

CALIB documentation built on Oct. 31, 2019, 3:45 a.m.