zoneRQ: Calculates the zone-based RawQ values

In harrisgm/GCSscore: GCSscore: an R package for microarray analysis for Affymetrix/Thermo Fisher arrays

Calculates the zone-based RawQ values

Description

This internally called function calculates the zone-based RawQ values. RawQ is a measure of the noise within a given zone on a microarray chip. This noise value is used in the error model contained in the GCS-score algorithm

Usage

zoneRQ(DT, affyCel, trim)

Arguments

DT	Internally generated data.table containing the .CEL data, generated from the list that is created by the affxparser package
affyCel	The .CEL file data, in list structure, as read in using the readCel function included in the affxparser package
trim	The internal setting for the trimmed mean of every probe grouping on the array. For 3' IVT arrays, the trim is set to 0.02 by default. For all newer WT-type arrays, the trim is set to 0.04 by default

Value

zoneRQ returns a numeric vector containing zone-based rawQ values for a given array

Examples

if (length(list.files(path = ".", pattern = "*.CEL")) != 0){

#Example of input, as the function would be called internally:
zoneRQ(DT, affyCel, trim)
}

harrisgm/GCSscore documentation built on Jan. 1, 2023, 12:04 a.m.