bacgroundCorrectSingleArray

List of beadLevelData objects (or single object).

NULL for normalization of all input b. Otherwise specifies logical vector of the length equals to the number of arrays in b or list of such vectors if b is a list of beadLevelData classes.

normalizationMod

channelBackground

Parameter of method stringency (default is 3).

Filtered beads will have weight 0 and non filtered weight 1.

channelBackgroundFilter

Represents vector to bitvise multiple to the channelBackgroundFilter vector.

channelAndVector

Background correction procedure selecting beads with background Intensity I_b |mean - I_b | > k*SD(I_bs) for exclusion, internal.

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.

bacgroundCorrectSingleArray: Data background correction.

Description

Usage

Arguments