computeZonenoise {sscore}R Documentation

Computes zone noise

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 rkennedy@vcu.edu

References

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


[Package sscore version 1.6.0 Index]