calcSF: calculates Scaling Factor (SF) values

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

calculates Scaling Factor (SF) values

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, clean.chip)

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
clean.chip	The clean chiptype name, based on the platform design package name.

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, clean.chip)
}

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