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Download Affymetrix Annotation Files

4.4 Download Affymetrix Annotation Files

Affymetrix NetAffx™ provides array design and annotation information for their GeneChip™ array results. You can sign up for and use the NetAffx™ Analysis Center through their website at http://www.affymetrix.com/.

SVS is able to communicate with NetAffx™ through a web service interface allowing you to download and update genetic marker map information mappable to Affymetrix data. See Affymetrix Files for importing Affymetrix data files.

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To import genetic marker map information from the Affymetrix NetAffx™ service, select the Download Affymetrix Annotations button from the Marker Maps dialog, Tools > Genetic Marker Maps, or by going to Download > Affymetrix Annotations. You will be prompted for login credentials for the NetAffx™ service. Login credentials can be freely obtained through registering on Affymetrix’s website. Your login credentials will be saved in the Global Program options and will be used for future NetAffx downloads. If the login credentials need to be changed this can be done by going to Tools > Global Program Options from the Program Welcome Screen.

Once authenticated, the latest annotation listings will be shown in the dialog (see Figure 23).

Select one or more annotation files and click Download to download, combine and sort the annotation listings into a map DSM file. Note that the 50k and 250k annotation files come in pairs. For example, be sure to select both Mapping50K_Hind240.na26.annot.csv and Mapping50K_Xba240.na26.annot.csv.
Once downloaded, the annotations will be combined and will show up in the Marker Maps folder as
Mapping50K_Hind240-Xba240_na26_annot20080709.dsm.

NOTE:

• If your Internet connection goes through a proxy requiring authentication, SVS may not be able to communicate with the Affymetrix NetAffx™ service directly. You may need to configure your proxy settings from the Global Options dialog. Strict firewalls may also preclude communication with NetAffx™.