gdcVoomNormalization {GDCRNATools} | R Documentation |
Normalize raw counts data by TMM implemented in edgeR
and then transform it by voom
in limma
gdcVoomNormalization(counts, filter = TRUE)
counts |
raw counts of RNA/miRNA expression data |
filter |
logical, whether to filter out low-expression genes.
If |
A dataframe or numeric matrix of TMM normalized and
voom
transformed expression values on
the log2 scale
Ruidong Li and Han Qu
Robinson MD, McCarthy DJ, Smyth GK. edgeR: a Bioconductor package
for differential expression analysis of digital gene expression data.
Bioinformatics. 2010 Jan 1;26(1):139-40.
Law CW, Chen Y, Shi W, Smyth GK. Voom: precision weights unlock
linear model analysis tools for RNA-seq read counts. Genome biology.
2014 Feb 3;15(2):R29.
####### Normalization ####### rnaMatrix <- matrix(sample(1:100,100), 4, 25) rnaExpr <- gdcVoomNormalization(counts=rnaMatrix, filter=FALSE)