# Documentation

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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

 `Data` Either 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. `NumZonesValue` Scalar 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`. `PercentValue` Value 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`. `SmoothFactorValue` Value 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`. `NoiseFracValue` Value that specifies the noise fraction, `NF`, such that the background-adjusted value is given by ```max((Intensity - WeightedBackground), NF*LocalNoiseEstimate)```. Default is `0.5`. `CDFValue` Either of the following:Character vector 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. `MaskValue` Logical 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

 `BackAdjustedData` Matrix or cell array of vectors containing background-adjusted probe intensity values. `ZoneStruct` MATLAB 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. `Background` Matrix 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

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This example uses sample data from the E. coli Antisense Genome Array. Download the data from Demo_Data_E-coli-antisense.zip. Extract the data files from the DTT archive using the Data Transfer Tool.

You also need to download Ecoli_ASv2.CDF library file for the E. coli Antisense Genome Array. You may already have these files if you have any Affymetrix GeneChip software installed on your machine. If not, get the library files by downloading and unzipping the E. coli Antisense Genome Array zip file.

Read the contents of a CEL file into a MATLAB structure.

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

Read the contents of a CDF file into a MATLAB structure.

```cdfStruct = affyread('C:\LibFiles\Ecoli_ASv2.CDF'); ```

Use the `zonebackadj` function to return a matrix or cell array of vectors containing the estimated background values for each probe.

```[baData,zones,background] = zonebackadj(celStruct,'cdf',cdfStruct); ```

Create a table of intensity values for the `argG_b3172_at` probe set.

```psvals = probesetvalues(celStruct, cdfStruct, 'argG_b3172_at',... 'background',background) ```
```psvals = 1.0e+03 * Columns 1 through 7 5.2120 0 0 0.0454 0.4300 0.1770 0.1690 5.2120 0.0010 0 0.0455 0.4310 0.1770 0.1273 5.2120 0.0020 0 0.0455 0.4320 0.1770 0.1270 5.2120 0.0030 0 0.0455 0.4330 0.1770 0.1333 5.2120 0.0040 0 0.0455 0.4340 0.1770 0.2123 5.2120 0.0050 0 0.0455 0.4350 0.1770 0.1495 5.2120 0.0060 0 0.0455 0.4360 0.1770 0.0503 5.2120 0.0070 0 0.0456 0.4370 0.1770 0.1525 5.2120 0.0080 0 0.0456 0.4380 0.1770 0.1645 5.2120 0.0090 0 0.0456 0.4390 0.1770 0.1260 5.2120 0.0100 0 0.0456 0.4400 0.1770 0.0540 5.2120 0.0110 0 0.0456 0.4410 0.1770 0.0833 5.2120 0.0120 0 0.0457 0.4420 0.1770 0.0955 5.2120 0.0130 0 0.0457 0.4430 0.1770 0.1100 5.2120 0.0140 0 0.0457 0.4440 0.1770 0.2510 Columns 8 through 14 0.0354 0.0250 0 0 0.4300 0.1780 0.1635 0.0218 0.0300 0 0 0.4310 0.1780 0.1003 0.0237 0.0300 0 0 0.4320 0.1780 0.1750 0.0259 0.0360 0 0 0.4330 0.1780 0.0940 0.0433 0.0360 0 0 0.4340 0.1780 0.1718 0.0275 0.0360 0 0 0.4350 0.1780 0.1540 0.0112 0.0300 0 0 0.4360 0.1780 0.0460 0.0377 0.0360 0 0 0.4370 0.1780 0.1070 0.0312 0.0360 0 0 0.4380 0.1780 0.0973 0.0234 0.0360 0 0 0.4390 0.1780 0.1213 0.0112 0.0360 0 0 0.4400 0.1780 0.0540 0.0174 0.0360 0 0 0.4410 0.1780 0.0623 0.0171 0.0300 0 0 0.4420 0.1780 0.0840 0.0196 0.0360 0 0 0.4430 0.1780 0.0925 0.0460 0.0360 0 0 0.4440 0.1780 0.1118 Columns 15 through 20 0.0241 0.0300 0 0 0.0010 0.0020 0.0146 0.0360 0 0 0.0010 0.0020 0.0286 0.0360 0 0 0.0010 0.0020 0.0227 0.0300 0 0 0.0010 0.0020 0.0365 0.0300 0 0 0.0010 0.0020 0.0303 0.0300 0 0 0.0010 0.0020 0.0098 0.0250 0 0 0.0010 0.0020 0.0210 0.0360 0 0 0.0010 0.0020 0.0219 0.0360 0 0 0.0010 0.0020 0.0253 0.0360 0 0 0.0010 0.0020 0.0129 0.0360 0 0 0.0010 0.0020 0.0125 0.0360 0 0 0.0010 0.0020 0.0186 0.0300 0 0 0.0010 0.0020 0.0220 0.0360 0 0 0.0010 0.0020 0.0207 0.0360 0 0 0.0010 0.0020 ```