GetNormalizedMat: Calculate normalized expression matrix

In EBSeq: An R package for gene and isoform differential expression analysis of RNA-seq data

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

The function will return a normalized matrix.

Author(s)

Ning Leng

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)

EBSeq documentation built on Nov. 8, 2020, 6:52 p.m.