singleArrayNormalize

Object beadLevelData from package beadarray

NULL for normalization of all input b. Otherwise specifies logical vector of the length equals to the number of arrays in b.

normalizationMod

channelNormalize

channelOutput

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).

channelInclude

This field must be sorted. It is a distribution of values to assign to ports.
By default this distribution is computed using meanDistribution function.

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

Package blima includes several algorithms for the preprocessing of Illumina microarray data. It focuses to the bead level analysis and provides novel approach to the quantile normalization of the vectors of unequal lengths. It provides variety of the methods for background correction including background subtraction, RMA like convolution and background outlier removal. It also implements variance stabilizing transformation on the bead level. There are also implemented methods for data summarization. It also provides the methods for performing T-tests on the detector (bead) level and on the probe level for differential expression testing.

Vojtech Kulvait

blima

Package for the preprocessing and analysis of the Illumina microarrays on the detector (bead) level.

singleArrayNormalize function

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).

This field must be sorted. It is a distribution of values to assign to ports.
By default this distribution is computed using meanDistribution function.

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

singleArrayNormalize: Bead level quantile normalization.

Description

Usage

Arguments