Bioinformatics Toolbox™

zonebackadj - Perform background adjustment on Affymetrix microarray probe-level data using zone-based method

Syntax

BackAdjustedData = zonebackadj(Data)
[BackAdjustedData, ZoneStruct] = zonebackadj(Data)
[BackAdjustedData, ZoneStruct, Background] = zonebackadj(Data)

... = zonebackadj(Data, ...'NumZones', NumZonesValue, ...)
... = zonebackadj(Data, ...'Percent', PercentValue, ...)
... = zonebackadj(Data, ...'SmoothFactor', SmoothFactorValue, ...)
... = zonebackadj(Data, ...'NoiseFrac', NoiseFracValue, ...)
... = zonebackadj(Data, ...'CDF', CDFValue, ...)
... = zonebackadj(Data, ...'Mask', MaskValue, ...)
... = zonebackadj(Data, ...'Showplot', ShowplotValue, ...)

Arguments

Return Values

Description

BackAdjustedData = zonebackadj(Data) returns the background-adjusted probe intensities from Data, which contains probe intensities from Affymetrix CEL files. Details of the background adjustment are described in Statistical Algorithms Description Document.

[BackAdjustedData, ZoneStruct] = zonebackadj(Data) also returns a structure containing the centers of the zones used to perform the background adjustment and the estimates of the background values at the center of each zone.

[BackAdjustedData, ZoneStruct, Background] = zonebackadj(Data) also returns a matrix or cell array of vectors containing the estimated background values for each probe.

... = zonebackadj(Data, ...'PropertyName', PropertyValue, ...) calls zonebackadj with optional properties that use property name/property value pairs. You can specify one or more properties in any order. Each PropertyName must be enclosed in single quotation marks and is case insensitive. These property name/property value pairs are as follows:

... = zonebackadj(Data, ...'NumZones', NumZonesValue, ...) specifies the number of zones to use in the background adjustment. NumZonesValue can be either a scalar that is a square number or a two-element array in which the first element specifies the number of rows and the second element specifies the number of columns in a nonsquare grid. Default is 16.

... = zonebackadj(Data, ...'Percent', PercentValue, ...) specifies a percentage, P, such that the lowest P percent of ranked intensity values from each zone is used to estimate the background for that zone. Default is 2.

... = zonebackadj(Data, ...'SmoothFactor', SmoothFactorValue, ...) specifies the smoothing factor used in the calculation of the weighted average of the contributions of each zone to the background of a point, thus providing a smooth transition between zones. Default is 100.

... = zonebackadj(Data, ...'NoiseFrac', NoiseFracValue, ...) specifies the noise fraction, such that the background-adjusted value is given by max((Intensity - WeightedBackground), NF*LocalNoiseEstimate), where NF is NoiseFracValue. Default is 0.5.

... = zonebackadj(Data, ...'CDF', CDFValue, ...) specifies an Affymetrix CDF library file or structure, which specifies control cells, which are not used in the background estimates.

... = zonebackadj(Data, ...'Mask', MaskValue, ...) specifies a logical vector of that specifies which cells to mask and not use in the background estimates. In the vector, 0 = not masked and 1 = masked. Defaults are the values in the Masked column of the Probes field of the CEL file.

... = zonebackadj(Data, ...'Showplot', ShowplotValue, ...) plots an image of the background estimates. Choices are true or false (default).

Examples

The following example uses a sample CEL file and CDF library file from the E. coli Antisense Genome array, which you can download from:

http://www.affymetrix.com/support/technical/sample_data/demo_data.affx

After you download the demo data, you will need the Affymetrix Data Transfer Tool to extract the CEL file from a DTT file. You can download the Affymetrix Data Transfer Tool from:

http://www.affymetrix.com/products/software/specific/dtt.affx

The following example assumes that the Ecoli-antisense-121502.CEL file is stored on the MATLAB search path or in the current directory. It also assumes that the associated CDF library file, Ecoli_ASv2.CDF, is stored at D:\Affymetrix\LibFiles\Ecoli.

1. Use the affyread function to read an Affymetrix CEL file and create celStruct, a MATLAB structure containing probe intensities for a single Affymetrix GeneChip.

   celStruct = affyread('Ecoli-antisense-121502.CEL');
   

2. Perform background adjustment on the probe intensities in the structure, excluding the probe intensities from the control cells on the chip.

    BackAdjMatrix = zonebackadj(celStruct, 'cdf',...
                   'D:\Affymetrix\LibFiles\Ecoli\Ecoli_ASv2.CDF');
   

References

[1] Statistical Algorithms Description Document, http://www.affymetrix.com/support/technical/whitepapers/ sadd_whitepaper.pdf

See Also

Bioinformatics Toolbox functions: affyinvarsetnorm, affyread, celintensityread, gcrma, gcrmabackadj, probelibraryinfo, probesetlink, probesetlookup, probesetvalues, quantilenorm, rmabackadj, rmasummary

traceplot

Method Reference