vstFromLumi

The standard deviation of the probe beads

nSupport

Estimate the background variance c3. Input should be variance according to article, not SD.

backgroundStd

lowCutoff

This function is derived from copy and paste of lumi::vst function. Since lumi package has extensive imports I decided to hardcode this function to the blima instead of importing lumi package.

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.

vstFromLumi: Function from LGPL lumi package 2.16.0

Description

Usage

Arguments

References