filterMicroRna: Filtering Genes

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

Description

Filter genes out according to their Quality Flag

Usage

filterMicroRna(ddNORM, 
	dd,
	control,
	IsGeneDetected,
	wellaboveNEG,
	limIsGeneDetected,
	limNEG,
	makePLOT,
	targets,
	verbose,
  	writeout) 

Arguments

ddNORM	uRNAList with the Total Gene Signal in log2 scale to be FILTERED out according to a Quality FLAG
dd	uRNAList, containing the output from readMicroRnaAFE
control	logical, if TRUE it removes controls
IsGeneDetected	logical, if TRUE it filters genes according to gIsGeneDetected Flag. Flag = 1, then gene is detected
wellaboveNEG	logical, if TRUE it filter genes whose expression is not above a limit value defined by the expression of negative controls. Limit= Mean(negative) + 1.5 x sd(negative)
limIsGeneDetected	for a given feature xi accros samples, is the minimum in at least one experimental condition with a IsGeneDetected-FLAG = 1 (Is Detected)
limNEG	for a given feature xi accros samples, is the minimum in at least one experimental condition with intensity > Limit established for negative controls (Mean + 1.5 x SD)
makePLOT	logical, if TRUE makes QC plots with the remaining signals
targets	data.frame with the targets structure
verbose	logical, if TRUE prints out output
writeout	logical, if TRUE writes out output files

Details

Agilent Feature Extraction software provides a flag for each spot that identifies different quantification errors of the signal. Quantification flags were used to filter out signals that did not reach a minimum established criterion of quality.

Value

The function returns a uRNAList containing the FILTERED data. In order to allow the tracking of those microRNAs that may have been filtered out from the original raw data, the following files are given:

NOCtrl\_exprs.txt: Log2 Normalized Total Gene Signals for the Non Control Genes NOCtrl\_FlagIsGeneDetected.txt: IsGeneDetected Flag for the Non Control Genes, 1 = detected IsNOTGeneDetected.txt: Genes that not are not detected according to IsGeneDetected Flag

Author(s)

Pedro Lopez-Romero

References

Agilent Feature Extraction Reference Guide http://www.Agilent.com

Examples

data(dd.micro,verbose=FALSE)
data(targets.micro,verbose=FALSE)
ddTGS=tgsMicroRna(dd.micro,half=TRUE,makePLOT=FALSE,verbose=FALSE)
ddNORM=tgsNormalization(ddTGS,'quantile',
                      makePLOTpre=FALSE,makePLOTpost=TRUE,targets.micro,verbose=FALSE)
ddPROC=filterMicroRna(ddNORM,
		      dd.micro,
                      control=TRUE,
                      IsGeneDetected=TRUE,
                      wellaboveNEG=FALSE,
                      limIsGeneDetected=50,
                      limNEG=25,
                      makePLOT=FALSE,
                      targets.micro,
		      verbose=FALSE,
		      writeout=FALSE)

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