computeRawQ: Computes RawQ

In sscore: S-Score Algorithm for Affymetrix Oligonucleotide Microarrays

Description

Computes the RawQ value of a single Affymetrix GeneChip

Usage

computeRawQ(fname, intensity, probe.index, probe.zoneID, bgCells, NumberZones, celfile.path = NULL)

Arguments

fname	character string with the filename of the GeneChip
intensity	vector of intensities for the GeneChip
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
celfile.path	character denoting the path for the *.CEL files specified in fname

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.