bg.parameters.ns {gcrma}R Documentation

Estimation of non-specific Binding Background Parameters

Description

An internal function to be used by gcrma

Usage

bg.parameters.ns(x,affinities,order.aff=NULL,Q=.25,nbreaks=40,
                             monotonize.mu=TRUE,
                             monotonize.sigma=FALSE)

Arguments

x PM or MM intensities after optical background correction, before non-specific-binding correction.
affinities Probe affinities for probes with known sequences.
order.aff The order of affinities. If NULL, it will be computed in this function.
Q Between 0 and 1. For given affinity level, the Q-th quantile of log intensities is taken as the mean of the background distribution for this affinity level.
nbreaks The number of strata of affinity levels.
monotonize.mu
monotonize.sigma

{Logical value, if TRUE, estimated background standard deviation if forced to be monotonic with probe affinity level.}

Value

a vector of same length as x.

Author(s)

Rafeal Irizarry, Zhijin (Jean) Wu

See Also

gcrma


[Package gcrma version 1.1.0 Index]