Is it possible to launch IGB as a stand alone program without having the machine networked? I know that it could be done once the data are acquired but could I do it right from the beginning, just opening IGB and loading a file locally?
Yes, but not easily. You need to get the IGB jar file which can be downloaded from the IGB page on affymetrix.com. You will probably also want to grab all the data in the quickload folder from:
http://netaffxdas.affymetrix.com/quickload_data/
Put the data in this folder on the local computer. Start up IGB using Java and the IGB jar file. Change the URL for the quickload folder (on QuickLoad tab, select Quickload Options) and point it to the local folder with the quickload data.
Please note that Affymetrix will provide limited technical support for this local IGB workflow. Additional features in IGB, such as the "Get Info" annotation retrieval function, require an active network connection to the Affymetrix web site. Users may not be aware of significant feature improvements and enhancements to IGB and updated sequence information and annotations when a local version of IGB is implemented. Local deployment should be used with discretion.