sscore (version 1.44.0)

computeAffxRawQ: Computes RawQ using affxparser routines

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

Value

the RawQ value for the given array

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.

References

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