filterMicroRna {AgiMicroRna} | R Documentation

## Filtering Genes

### 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)

[Package AgiMicroRna version 2.38.0 Index]