filter.wellaboveNEG {Agi4x44PreProcess} | R Documentation

## probes.filter (Internal function)

### Description

An internal function to be used by `filter.probes`

### Usage

    filter.wellaboveNEG(ddFILT, ddNORM, limNEG, SDtimes, ManuelaGO, targets, annotation.package)

### Arguments

`ddFILT` | A RGlist in log2 scale, normally after Normalization and other filtering steps
`ddNORM` | An RGlist normally containing NORMALIZED data in log2 scale
`limNEG` | for a given feature xi accros samples, is the minimum in a experimental condition with a intensity > Limit established for negative controls (Mean + 1.5 x SD)
`SDtimes` | 1.5 in 'Mean + 1.5 x SD'. It is fixed to 1.5 in 'filter.probes'
`ManuelaGO` | logical, if a known annotation package is available then it is `TRUE`
`targets` | data.frame with the target structure
`annotation.package` | a character specifying the AGI annotation package: 'hgug4112a.db','mgug4122a.db'

### Details

For each feature we can demand a minimum signal value that have to be reached at least for a p in one of the experimental conditions. The minimum limit is established as Mean Negative Controls + 1.5*(Std. dev.Negative Controls). Normally, after filtering by the WellAboveBG and IsFound criteria, all probes are well above negative controls.

### Value

An RGlist with signals that are above NEG controls (according to the correspondind AFE flag and the filtering options). It also writes an output file (IsNOTWellAboveNEG.txt) that contains probes that were filtered out because they were not distinguishable from negative controls.

### Author(s)

Pedro Lopez-Romero

### See Also

`filter.probes`

### Examples

    ## Not run:
            data(dd)
            data(targets)
            library(hgug4112a.db)
            ddNORM=BGandNorm(dd,BGmethod='half',NORMmethod='quantile',
                            foreground='MeanSignal',background='BGMedianSignal',
                            offset=50,makePLOTpre=FALSE,makePLOTpost=FALSE)
            ddFILT=filter.wellaboveBG(ddNORM,75,TRUE,targets,"hgug4112a.db")
            ddFILT2=filter.wellaboveNEG(ddFILT,ddNORM,75,SDtimes=1.5,TRUE,targets,"hgug4112a.db")
            dim(ddFILT2)
    ## End(Not run)

[Package Agi4x44PreProcess version 1.2.0 Index]