computeAffxRawQ: Computes RawQ using affxparser routines

In sscore: S-Score Algorithm for Affymetrix Oligonucleotide Microarrays

Description

Computes the RawQ value of a single Affymetrix GeneChip

Usage

computeAffxRawQ(intensity, stdvs, pixels, probe.index, probe.zoneID, bgCells, NumberZones)

Arguments

intensity	vector of intensities for the GeneChip
stdvs	matrix of standard deviations for probe intensities from *.CEL file
pixels	matrix of number of pixels for probe intensities from *.CEL file
probe.index	vector of indices for each probe
probe.zoneID	vector of zone ID numbers for each probe
bgCells	number of background cells for the GeneChip
NumberZones	number of zones on the GeneChip

Details

Calculates RawQ using the algorithms described in the Affymetrix Statistical Algorithms Description Document for a single GeneChip. This is an internal function that will generally not be accessed directly.

Value

the RawQ value for the given array

Note

Based on Affymetrix MAS5 Statistical SDK source code http://www.affymetrix.com/Auth/support/developer/stat_sdk/STAT_SDK_source.zip, as well as C++ code by Li Zhang and Delphi code by Robnet Kerns

Author(s)

Richard Kennedy [e-mail]

References

Affymetrix (2002) Statistical Algorithms Description Document, Affymetrix Inc., Santa Clara, CA, whitepaper. http://www.affymetrix.com/support/technical/whitepapers/sadd_whitepaper.pdf

sscore documentation built on Nov. 8, 2020, 5:28 p.m.