computeZonenoise: Computes zone noise

In sscore: S-Score Algorithm for Affymetrix Oligonucleotide Microarrays

Description

Computes the noise (average standard error) of the probe intensities for a single Affymetrix GeneChip

Usage

computeZonenoise(index, intensity, stdv, npixels, bgCells)

Arguments

index	vector of indices for probes in the given zone
intensity	vector of intensities for the GeneChip
stdv	vector of standard deviations for the GeneChip
npixels	vector containing number of pixels for each probe of the GeneChip
bgCells	number of background cells on the GeneChip

Details

Calculates the noise (average standard error) of the probes in a given zone, 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 noise of the probes 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.