calcSF: calculates Scaling Factor (SF) values

In mfmiles/Sscore2: Sscore2: an R package for microarray analysis for Affymetrix/Thermo Fisher arrays

Description

This internally called function calculates the scaling factor (SF) values for Affymetrix microarrays, for use in computing GCS-score values

Usage

calcSF(diff, probetab, trim)

Arguments

diff	The GC-content background corrected probe groupings for every probesetID or transcriptionclusterID on the given array type. This is generated internally by the computeSscore function
probetab	The internal datafile that contains the probe groupings and annotations for each array type and method type
trim	The internal setting for the trimmed mean of every probe grouping on the array, as used in the calculation of SF. 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

calcSF returns a numeric SF value for a given CEL file

Examples

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

#Example of input, as the function would be called internally:
calcSF(diff, probetab, trim)
}

mfmiles/Sscore2 documentation built on Oct. 1, 2019, 6:04 a.m.