In TweetDeck I have several saved searches. This would cause a pop-up to come up constantly, so I turned off the alerts. However, there are some things I want to be alerted to. How can I enable alerts only for people that I'm following and disable alerts for my searches?
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Click "Settings" (wrench in the upper right). In the settings dialog, click "Notifications", then click "Advanced Options for columns". That will make a bunch of checkboxes appear, which you can use to enable or disable the alerts on a column-by-column basis.

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