alpine (version 0.99.1)

normalizeDESeq: DESeq median ratio normalization for matrix

Description

Simple implementation of DESeq median ratio normalization

Usage

normalizeDESeq(mat, cutoff)

Arguments

mat

a matrix of numeric values

cutoff

a numeric value to be used as the cutoff for the row means of mat. Only rows with row mean larger than cutoff are used for calculating the size factors

Value

a matrix with the median ratio size factors divided out

References

Anders, S. and Huber, W., Differential expression analysis for sequence count data. Genome Biology (2010) doi: 10.1186/gb-2010-11-10-r106

Examples

x <- runif(50,1,100)
mat <- cbind(x, 2*x, 3*x)
norm.mat <- normalizeDESeq(mat, 5)