Documentation

probesetlink

Display probe set information on NetAffx Web site

Syntax

probesetlink(AffyStruct, PS)
URL = probesetlink(AffyStruct, PS)

probesetlink(AffyStruct, PS, ...'Source', SourceValue, ...)
probesetlink(AffyStruct, PS, ...'Browser', BrowserValue, ...)
URL = probesetlink(AffyStruct, PS, ...'NoDisplay', NoDisplayValue, ...)

Input Arguments

AffyStructStructure created by the affyread function from an Affymetrix® CHP file or an Affymetrix CDF library file.
PSProbe set index or the probe set ID/name.
SourceValueControls the linking to the data source (for example, GenBank® or Flybase) for the probe set (instead of linking to the NetAffx™ Web site). Choices are true or false (default).

    Note:   This property requires the GIN library file associated with the CHP or CDF file to be located in the same folder as the CDF library file.

BrowserValueControls the display of the probe set information in your system's default Web browser. Choices are true or false (default).
NoDisplayValueControls the return of URL without opening a Web browser. Choices are true or false (default).

Output Arguments

URLURL for the probe set information.

Description

probesetlink(AffyStruct, PS) opens a Web Browser window displaying information on the NetAffx Web site about a probe set specified by PS, a probe set index or the probe set ID/name, and AffyStruct, a structure created from an Affymetrix CHP file or Affymetrix CDF library file.

URL = probesetlink(AffyStruct, PS) also returns the URL (linking to the NetAffx Web site) for the probe set information.

probesetlink(AffyStruct, PS, ...'PropertyName', PropertyValue, ...) calls probesetlink 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:


probesetlink(AffyStruct, PS, ...'Source', SourceValue, ...)
controls the linking to the data source (for example, GenBank or Flybase) for the probe set (instead of linking to the NetAffx Web site). Choices are true or false (default).

    Note:   The 'Source' property requires the GIN library file associated with the CHP or CDF file to be located in the same folder as the CDF library file.

probesetlink(AffyStruct, PS, ...'Browser', BrowserValue, ...) controls the display of the probe set information in your system's default Web browser. Choices are true or false (default).

URL = probesetlink(AffyStruct, PS, ...'NoDisplay', NoDisplayValue, ...) controls the return of the URL without opening a Web browser. Choices are true or false (default).

    Note:   The NetAffx Web site requires you to register and provide a user name and password.

Examples

The following example uses a sample CHP file and the 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 CHP 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.CHP 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. Read the contents of a CHP file into a MATLAB structure.

    chpStruct = affyread('Ecoli-antisense-121502.CHP',...
                 'D:\Affymetrix\LibFiles\Ecoli');
  2. Display information from the NetAffx Web site for the argG_b3172_at probe set.

    probesetlink(chpStruct,'argG_b3172_at')
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