2. Import Affymetrix Marker Map

Before you can begin creating files that can be viewed in Affymetrix’s GTC Browser, you first need to import an appropriate marker map. Because this tutorial focuses on analyzing Affymetrix 500K data, you need to import the Affymetrix 500K marker map (annotation file).

The latest Affymetrix marker maps can be downloaded using the Affymetrix NetAffx service in HelixTree. To access this feature from the main Project Navigation window, select >File >Import Data >Download Affymetrix Marker Map. You will be prompted for your Affymetrix NetAffx login information, which can be freely obtained by registering on Affymetrix’s website:

https://www.affymetrix.com/analysis/netaffx/index.affx

After entering your NetAffx login information, the Download Annotations window will appear listing various Affymetrix annotation files (Figure 1).

IMPORTANT: There are actually two annotation files for each of the 500K, 5.0, and 6.0 files (500K = NSP + STY, SNP 5.0 and 6.0 = SNP + CN probes). For each file set, both corresponding annotation files need to be downloaded simultaneously for HelixTree to properly merge them. To do this, highlight both annotation files (as seen in Figure 1). Make sure the box Import into project when downloaded is checked, and click Download. If you downloaded the annotation files previously, they should show up as a single merged file in the lower section of the window. If this is the case, you can just highlight that file and click Load Into Project.

Once the marker map is loaded it will show up as a node in the Project Navigation window.