filter.NonUnifOL {Agi4x44PreProcess}R Documentation

probes.filter (Internal function)

Description

An internal function to be used by filter.probes

Usage

filter.NonUnifOL(ddFILT, limNonUnifOL, ManuelaGO, targets, annotation.package)

Arguments

ddFILT an RGlist object
limNonUnifOL for a given feature xi accros samples, is the maximum in a experimental condition with a saturation-FLAG = 1 (Is Non Uni OL)
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

To keep good quality probes, we filtered out probes that has more than y in at least one experimental condition with a flag indicating the presence of non-uniformity outlier. A feature is non-uniform outlier if its pixel noise exceeds a threshold established for a uniform feature. 1 indicates Feature is a non-uniformity outlier.

Value

An RGlist with probes that are not non-uniformity Outlier (according to the correspondind AFE flag and the filtering options). It also writes an output file (IsFeatNonUnifOL.txt) that contains probes that were filtered out because they were considered non-uniformity Outlier.

Author(s)

Pedro Lopez-Romero

See Also

filter.probes

Examples

## Not run: 
        data(dd)
        data(targets)
        library(hgug4112a.db)
        ddFILT=filter.NonUnifOL(dd,25,TRUE,targets,"hgug4112a.db")
        dim(ddFILT)
## End(Not run)

[Package Agi4x44PreProcess version 1.2.0 Index]