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]