TCGAbiolinks (version 1.2.5)

TCGAanalyze_Normalization: normalization mRNA transcripts and miRNA using EDASeq package.

Description

TCGAanalyze_Normalization allows user to normalize mRNA transcripts and miRNA, using EDASeq package.

Normalization for RNA-Seq Numerical and graphical summaries of RNA-Seq read data. Within-lane normalization procedures to adjust for GC-content effect (or other gene-level effects) on read counts: loess robust local regression, global-scaling, and full-quantile normalization (Risso et al., 2011). Between-lane normalization procedures to adjust for distributional differences between lanes (e.g., sequencing depth): global-scaling and full-quantile normalization (Bullard et al., 2010).

For istance returns all mRNA or miRNA with mean across all samples, higher than the threshold defined quantile mean across all samples.

TCGAanalyze_Normalization performs normalization using following functions from EDASeq

1. EDASeq::newSeqExpressionSet
2. EDASeq::withinLaneNormalization
3. EDASeq::betweenLaneNormalization
4. EDASeq::counts

Usage

TCGAanalyze_Normalization(tabDF, geneInfo, method = "geneLength")

Arguments

tabDF

Rnaseq numeric matrix, each row represents a gene, each column represents a sample

geneInfo

Information matrix of 20531 genes about geneLength and gcContent

method

is method of normalization such as 'gcContent' or 'geneLength'

Value

Rnaseq matrix normalized with counts slot holds the count data as a matrix of non-negative integer count values, one row for each observational unit (gene or the like), and one column for each sample.

Examples

dataNorm <- TCGAbiolinks::TCGAanalyze_Normalization(dataBRCA, geneInfo)