tgsNormalization: Normalization Between Arrays

In AgiMicroRna: Processing and Differential Expression Analysis of Agilent microRNA chips

Description

Normalization between arrays of the Total Gene Signal. The function is a wrapper of the 'limma' 'normalizeBetweenArrays' with ('none','quantile','scale') methods

Usage

tgsNormalization(ddTGS, NORMmethod = "quantile", makePLOTpre = FALSE, makePLOTpost = FALSE, targets,verbose=FALSE)

Arguments

ddTGS	uRNAList, containing the output from tgsMicroRna
NORMmethod	character specifying the normalization method, 'none','quantile','scale'. The default is quantile
makePLOTpre	logical, if TRUE QC plots with the Raw Total Gene Signal are displayed
makePLOTpost	logical, if TRUE QC plots with the Normalized Total Gene Signal are displayed
targets	data.frame with the target structure
verbose	logical, if TRUE prints out output

Value

A uRNAList object containing the Normalized Total Gene Signal in log 2 scale

Author(s)

Pedro Lopez-Romero

References

Smyth, G. K. (2005). Limma: linear models for microarray data. In: 'Bioinformatics and Computational Biology Solutions Using R and Bioconductor'. R. Gentleman, V. Carey, S. Dudoit, R. Irizarry, W. Huber (eds), Springer, New York, pages 397 - 420

Smyth, G. K., and Speed, T. P. (2003). Normalization of cDNA microarray data. Methods 31, 265-273.

Examples

## Not run: 
data(dd.micro)
data(targets.micro)
ddTGS=tgsMicroRna(dd.micro,half=TRUE,makePLOT=FALSE,verbose=FALSE)

ddNORM=tgsNormalization(ddTGS,'quantile',
                makePLOTpre=FALSE,makePLOTpost=TRUE,targets.micro,verbose=TRUE)
graphics.off()


## End(Not run)

AgiMicroRna documentation built on Nov. 8, 2020, 5:25 p.m.