filter.isfound {Agi4x44PreProcess} | R Documentation

## probes.filter (Internal function)

### Description

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

### Usage

    filter.isfound(ddFILT, limISF, ManuelaGO, targets, annotation.package)

### Arguments

`ddFILT` |
`limISF` | for a given spot xi accros samples, is the minimum in a experimental condition with a isfound-FLAG = 1 (Is Found)
`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 found. 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 found. A spot is considered Found if two conditions are true: 1) the difference between spot signal and the local background signal is more than 1.5 times the local background noise and 2) the spot diameter is at least 0.30 times the nominal spot diameter. A Boolean variable is used to flag found features. 1 = IsFound

### Value

An RGlist with probes that are found (according to the correspondind AFE flag and the filtering options). It also writes an output file (IsNOTFound.txt) that contains probes that were filtered out because were NOT FOUND.

### Author(s)

Pedro Lopez-Romero

### See Also

`filter.probes`

### Examples

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

[Package Agi4x44PreProcess version 1.4.0 Index]