EBSeq (version 1.12.0)

GetNormalizedMat: Calculate normalized expression matrix

Description

'GetNormalizedMat' calculates the normalized expression matrix. (Note: this matrix is only used for visualization etc. EBTes and EBMultiTest request *un-adjusted* expressions and normalization factors.)

Usage

GetNormalizedMat(Data, Sizes)

Arguments

Data

The data matrix with transcripts in rows and lanes in columns.

Sizes

A vector contains the normalization factor for each lane.

Value

References

Ning Leng, John A. Dawson, James A. Thomson, Victor Ruotti, Anna I. Rissman, Bart M.G. Smits, Jill D. Haag, Michael N. Gould, Ron M. Stewart, and Christina Kendziorski. EBSeq: An empirical Bayes hierarchical model for inference in RNA-seq experiments. Bioinformatics (2013)

Examples

data(GeneMat)
str(GeneMat)
Sizes = MedianNorm(GeneMat)
NormData = GetNormalizedMat(GeneMat, Sizes)