xieBacgroundCorrectSingleArray

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

normalizationMod

Vector of addresses of negative control probes on array

negativeArrayAddresses

channelCorrect

Result channel, if this channel exists it will be overwritten.

channelResult

This field allows user to set channel with weights which have to be from 0,1.
All zero weighted items are excluded from summarization.
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

INTERNAL This function is not intended for direct use.
Background correction according to non parametric estimator in
Xie, Yang, Xinlei Wang, and Michael Story. 
"Statistical Methods of Background Correction for Illumina BeadArray Data."
Bioinformatics 25, no. 6 (March 15, 2009): 751-57. doi:10.1093/bioinformatics/btp040.
The method is applied on the bead level.

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.

xieBacgroundCorrectSingleArray function

This field allows user to set channel with weights which have to be from {0,1}.
All zero weighted items are excluded from summarization.
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).

INTERNAL This function is not intended for direct use.
Background correction according to non parametric estimator in
Xie, Yang, Xinlei Wang, and Michael Story. 
"Statistical Methods of Background Correction for Illumina BeadArray Data."
Bioinformatics 25, no. 6 (March 15, 2009): 751-57. doi:10.1093/bioinformatics/btp040.
The method is applied on the bead level.

xieBacgroundCorrectSingleArray: INTERNAL FUNCTION Xie background correct.

Description

Usage

Arguments