Sometimes, when I save and close a gel window, the program asks me "Settings have been changed. Do you want to use the current settings as new defaults?" What does this mean?
The question "Settings have been changed. Do you want to use the current settings as new defaults?" is asked when you have changed something to the gel processing settings of the current fingerprint type. This can be the OD range, the background subtraction, spot removal, filtering, curve resolution, band search settings, etc. When you answer Yes, the changed settings will apply to all new gels that will be processed under this fingerprint type, but not to the gels already processed in the database.
So, if you had to change the settings because the current gel is aberrant, you should answer No to the question, in order to keep the default settings for the next gels. If you made some improvements to the settings which you believe will facilitate or improve the processing of all subsequent gels, you may answer Yes. Keep in mind, however, that changing certain settings may cause new gels to become less compatible with previously processed gels.