mismatch: Calculates mismatch values for probes

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

Calculates mismatch values for probes

Description

This internally called function calculates the background correction for each probe based on the median intensity of all background probes with the same GC-content of as the target probe in question

Usage

mismatch(probes, bgp, intensity)

Arguments

probes	probe indicies for target probes. Each probe index contains the gc-content of the probe
bgp	contains probe location (indicies), GC-content, and annotations of the background probes of a given chip type. For WT-type arrays, the bgp consists of 16,943 antigenomic background probes. For 3' IVT arrays, the mismatch (MM) probes are used to calculate the bgp list in both methods
intensity	The intensities value of the bgp probes as read in from the .CEL file

Details

This internally called function calculates the probe background correction based on the median intensity of all background probes with the same gc-content of as the target probe in question

Value

mismatch returns a numeric vector containing the gc-content based background correction for every probe included in the analysis

Examples

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

#Example of input, as the function would be called internally:
mismatch(probes, bgp, intensity)
}

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