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 1.2.0 Index]