aggregateAndPreprocess

Two column matrix to agregate with columns "ProbeID" and quality.

quality

Function of input data trasformation, default is NULL. Any function which for input value returns transformed value may be supplied. T-test then will be evaluated on transformed data, consider use log2TranformPositive.

transformation

This function is not intended to direct use. It helps perform work of doProbeTTests function. For each probe it prints mean and sd of an quality.

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.

aggregateAndPreprocess: Aggregate data

Description

Usage

Arguments