fitRockeDurbin: Fit Rocke-Durbin Error Model

In GESTr: Gene Expression State Transformation

Description

Estimates Rocke-Durbin error model parameters for a gene expression dataset.

Usage

fitRockeDurbin(x,theta)

Arguments

x	Numeric data input array to be transformed into universal gene expression 'state' scale. Probes/genes should be in rows, samples/conditions in columns.
theta	Numeric value specifying Normal distribution quantile for identifying groups samples similar enough to be treated as replicates

Details

Estimates error model parameters for Rocke-Durbin model of microarray measurement errors. The model comprises three parameters to be estimated: the background measurement level, an intensity-dependent error term and an intensity-independent error term. This function finds groups of suitably-similar samples from the dataset to be treated as replicates, and estimates model parameters from constitutively-low and constitutively-high measurements.

Value

A list with 3 named components:

alpha	background measurement
sd_epsilon	standard deviation of intensity-dependent errors
sd_eta	standard deviation of intensity-independent errors

Author(s)

Ed Curry [e-mail]

Examples

## Not run: data(GESTr)
## Not run: RDparameters <- fitRockeDurbin(ABIdata,theta=0.05)

GESTr documentation built on May 2, 2019, 9:37 a.m.