Using NetAffx

When you first enter NetAffx you will be asked to login with your email address and a password you create. You can connect to NetAffx from Microarray Suite and get information for a single probe at a time (right-click on a probe set ID in the Pivot window and go to the External Database NetAffx, or use the Info button for the selected probe on one of the Graph views). You can also save a probe list, list of Gene Names, or a list of accession numbers and upload it into the NetAffx Batch Query form. By default you will see information about the Array, Probe, Public Domain Annotations, Functional Annotations, and the Target Sequence. It is possible to create your own customized views in which you select the information that will be returned from a query. As an example, here are the steps to download ATG ID Numbers for the Arabidopsis ATH1 probes:

Go to Affymetrix web site and click on Analysis, then Interactive Query. You must login if you have not yet signed on.

Select the Views Tab, enter your new View name and select the correct Target databank in the left box. Then press Create New View. You will then be able to select the information you want to see in your new view. For example, one might choose Title, AGI ID, and Go Biological Process. When you have made your choices, press Save View. This view will be available in the Views list until you decide to Delete it.

To apply your view, first go back to the Top Page, select the correct Target under 'Affymetrix Array Annotations/Target Sequences', then press 'All Entries'. The next page will show the Annotation Table View for each probe. Select your custom view from the View list and press 'View'. The information specified in your view will be displayed for each probe set. You may have to go forward a few pages since the control probes will not have anything listed in your view.

If you would like to save this information to an Excel file, press 'Save'. From the next screen, choose 'Download to Computer', then press 'Save'. This download may take a few minutes, and when it is finished you'll be prompted to enter the name of the file to save it in. The information will be saved in a tab-delimited file.

If you have difficulty using Affymetrix software or NetAffx, you may call their technical support line at 1-888-DNA-CHIP (1-888-362-2447).