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, ...)

Input Arguments

DataEither of the following:
  • MATLAB® structure containing probe intensities from an Affymetrix® CEL file, such as returned by affyread when used to read a CEL file.

  • Array of MATLAB structures containing probe intensities from multiple Affymetrix CEL files.

NumZonesValueScalar or two-element vector that specifies the number of zones to use in the background adjustment. If a scalar, it must be a square number. If a two-element vector, the first element specifies the number of rows and the second element specifies the number of columns in a nonsquare grid. Default is 16.
PercentValueValue that 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.
SmoothFactorValueValue that specifies the smoothing factor used in the calculation of the weighted average of the contributions of each zone to the background of a point. Default is 100.
NoiseFracValueValue that specifies the noise fraction, NF, such that the background-adjusted value is given by max((Intensity - WeightedBackground), NF*LocalNoiseEstimate). Default is 0.5.
CDFValueEither of the following:
  • String specifying a file name or path and file name of an Affymetrix CDF library file. If you specify only a file name, the file must be on the MATLAB search path or in the current folder.

  • MATLAB structure containing information from an Affymetrix CDF library file, such as returned by affyread when used to read a CDF file.

The CDF library file or structure specifies control cells, which are not used in the background estimates.
MaskValueLogical vector 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.
ShowplotValue

Controls the plotting of an image of the background estimates. Choices are true or false (default).

Output Arguments

BackAdjustedDataMatrix or cell array of vectors containing background-adjusted probe intensity values.
ZoneStructMATLAB 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.
BackgroundMatrix or cell array of vectors containing the estimated background values for each probe.

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 sample 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/browse/products.jsp?productId=131431&navMode=34000&navAction=jump&aId=productsNav

The following example assumes that the Ecoli-antisense-121502.CEL file is stored on the MATLAB search path or in the current folder. 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

Was this topic helpful?