filter.wellaboveBG {Agi4x44PreProcess} | R Documentation

## probes.filter (Internal function)

### Description

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

### Usage

    filter.wellaboveBG(ddFILT, limWellAbove, ManuelaGO, targets, annotation.package)

### Arguments

`ddFILT` | an RGlist object
`limWellAbove` | for a given feature xi accros samples, is the minimum in an experimental condition with a wellaboveBG-FLAG = 1 (Is Well Above BG)
`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

It eliminates signals that were not distinguishable from the local background signal. The filtering is based on the FLAG given by the AFE as follows: For a feature = xi accross all the samples, we demand that at least p spots for that feature, in at least one experimental condition, had a quantification flag denoting that the signal is distinguishable from background. AFE produces a Boolean flag indicating if a spot is WellAbove Background (Flag = 1) or not (Flag = 0). A spot reaches a Flag = 1 if IsPosAndSignif and additionally the gBGSubSignal is greater than 2.6*g(r)BG_SD. IsPosAndSignif uses a Boolean flag, established via a 2-sided t-test, indicates if the mean signal of a spot is greater than the corresponding background. 1 indicates spot is positive and significant above background.

### Value

An RGlist with probes that are above BG (according to the correspondind AFE flag and the filtering options). It also writes an output file (IsNOTWellAboveBG.txt) that contains the probes that were filtered out because they were not distinguishable from the local background signal.

### Author(s)

Pedro Lopez-Romero

### See Also

`filter.probes`

### Examples

    ## Not run:
            data(dd)
            data(targets)
            library(hgug4112a.db)
            ddFILT=filter.wellaboveBG(dd,75,TRUE,targets,"hgug4112a.db")
            dim(ddFILT)
    ## End(Not run)

[Package Agi4x44PreProcess version 1.2.0 Index]