Page History

...

_First, replace the following line in the original_ _source file:_

import gov.nih.nci.caarray.util.UsernameHolder;

...

1. Make sure that your Java classpath includes the updated client library (this is taken care of if you run the example using Ant as shown below).
2. Upload the array design files for the Affymetrix Mapping 250K Nsp and Sty chips into caArray using caArray web interface.
3. Create a directory called arraydata in the same location as that in which you execute the client-side program.
4. Copy a few Affymetrix 250K data files (CEL, CHP) and optionally MAGE-TAB IDF and SDRF files to the arraydata directory .
5. Run command below:

   Code Block
   $ ant compile-example $ ant run-example

Scenario 2. Upload Affymetrix Expression Files

...

• Uploaded the related array designs into caArray web interface.
• Modify the values for the following constants in CaArrayImporterExample.java (please note that the values provided are for illustration purpose only and need to be replaced):

  Code Block

  private static final String SERVER_HOST = "yourCaArrayServerHost"; private static final int SERVER_JNDI_PORT = 31099; private static final String USERNAME = "yourUsername"; private static final String PASSWORD = "yourPswd"; public static String TITLE = "Test Affymetrix Expression Project"; public static String PROVIDER = "Affymetrix"; public static String ASSAY_TYPE = "Gene Expression"; public static String[) ARRAY_DESIGNS = new String(] \{ "HG-U133_Plus_2" \};

• If you have your data files stored under a directory (an example: C:/data/caarray/MAGEdataFiles) different from the arraydata created in scenario 1, please replace the directory arraydata with the path to that directory as shown below in the function "main" (it can be either relative or absolute path):

  Code Block
  client.uploadFiles(project, "C:/data/caarray/MAGEdataFiles");

• Copy a few Affymetrix HG-U133_Plus_2 data files (CEL, CHP) and optionally MAGE-TAB IDF and SDRF files to the C:/data/caarray/MAGEdataFiles directory .
• Run the command below:

  Code Block
  $ ant compile-example $ ant run-example

Have a comment?

...