Setting up Array Studio for importing of a custom Affymetrix chip is a multi-step process.  First, the user must import the .cdf file obtained from Affymetrix, by going to the Tools Menu | Misc | Generate Custom Affymetrix CDF Libary. This will prompt the user for the location of the .cdf file, and will create the specialized Affymetrix information in the user's home Omicsoft folder.  

Next, the user needs to save a copy of the annotation file obtained from Affymetrix, as a .CSV file.  Then, go to Tools Menu | Annotation |Build Custom Annotation (NOT Build Custom Affymetrix Annotation--that is a different module, used by large companies that have their own internal Affymetrix annotation).

At this point, choose Browse for the Primary annotation CSV file and choose the CSV file containing the annotation.  Next, and this is important, set the Annotation source as Affymetrix and the Annotation name as the chip name (it should exactly match the chip name from the .cdf file used earlier).

The user has additional options for other .csv files that can be used to generate custom links in the annotation (above and beyond what is provide by Array Studio for Affymetrix chips).  For more information, contact support@omicsoft.com.

Click OK to build the annotation.  Now, when importing .CEL files from your custom chips, your annotation will be imported automatically.