filter.saturated {Agi4x44PreProcess} | R Documentation

## probes.filter (Internal function)

### Description

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

### Usage

    filter.saturated(ddFILT, limSAT, ManuelaGO, targets, annotation.package)

### Arguments

`ddFILT` | an RGlist object
`limSAT` | for a given feature xi accros samples, is the minimum in a experimental condition with a saturation-FLAG = 0 (Non Saturated)
`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 saturated signals. 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 not saturated. AFE produces a Boolean flag indicating whether a spot is saturated (Flag = 1) or not saturated (Flag = 0). A spot is saturated IF 50 threshold.

### Value

An RGlist with probes that are not saturated (according to the correspondind AFE flag and the filtering options). It also writes an output file (IsSaturated.txt) that contains probes that were saturated.

### Author(s)

Pedro Lopez-Romero

### See Also

`filter.probes`

### Examples

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

    ## End(Not run)

[Package Agi4x44PreProcess version 1.4.0 Index]