singleArrayNormalize: Bead level quantile normalization.

In blima: Tools for the preprocessing and analysis of the Illumina microarrays on the detector (bead) level

Description

This function does quantile normalization of object beadLevelData from package beadarray. Internal function not intended to direct use. Please use quantileNormalize.

Usage

singleArrayNormalize(b, normalizationMod = NULL, channelNormalize = "Grn", 
    channelOutput = "qua", channelInclude = NULL, dst)

Arguments

b	Object beadLevelData from package beadarray
normalizationMod	NULL for normalization of all input b. Otherwise specifies logical vector of the length equals to the number of arrays in b.
channelNormalize	Name of channel to normalize.
channelOutput	Name of output normalized channel.
channelInclude	This field allows user to set channel with weights which have to be in 0,1. All zero weighted items are excluded from quantile normalization and the value asigned to such probes is a close to value which would be assigned to them if not being excluded. You can turn this off by setting this NULL. This option may be used together with bacgroundCorrect method or/and with beadarray QC (defaults to NULL).
dst	This field must be sorted. It is a distribution of values to assign to ports. By default this distribution is computed using meanDistribution function.

Author(s)

Vojt<c4><9b>ch Kulvait

blima documentation built on Nov. 8, 2020, 8:15 p.m.