getErrorModel: Estimates error model parameters var0 (basal variance) and...

Description Usage Arguments Details Value Author(s)

View source: R/getErrorModel.R


The method is based on a maximum-likelihood estimation. The model prediction is the expected variance given the signal, depending on var0 and varR.


getErrorModel(dataexpression, verbose=FALSE)



data.frame, standard output from RPPanalyzer's write.Data.


logical, if TRUE, the function prints out additional information and produces a PDF file in the working directory with the signal vs. variance plots.


The empirical variance estimator is χ^2 distributed with n-2 degrees of freedom, where n is the number of technical replicates. The estimated error parameters maximize the corresponding log-likelihood function. At the moment, the code assumes n=3. For cases n>3, the error parameters are slightly overestimated, thus, providing a conservative result. The explicit error model is

σ^2(S) = σ_0^2 + S^2σ_R^2 = var0 + varR S^2

where S is the signal strength.



with columns "slide" (factor, the slide names), "ab" (factor, the antibody/target names), "time" (numeric, the time points), "signal" (numeric, signal values), "var0" (numeric, error parameter for the constant error, equivalent to sigma0^2), "varR" (numeric, error parameter for the relative error, equivalent to sigmaR^2) and other columns depending on the input data.frame


Daniel Kaschek, Physikalisches Institut, Uni Freiburg. Email:

RPPanalyzer documentation built on Dec. 17, 2020, 5:10 p.m.