Use entity_metadata_wrapper to access field_collections

Both modules, entity and field_collection, are programmed by the same guy. As one would expect, they work together very well.

There is a field collection called "field_user_settings" on the user entity. The field collections holds a field called "field_notify_reply" (which is a Boolean).
This way you can access the value of the "field_notify_reply" given an user-id.

$author = user_load(12);
$author_wrapper = entity_metadata_wrapper('user', $author);
print $author_wrapper->get('field_user_settings')->field_notify_reply->value(); //prints either 0 or 1

You can also set the value

$author = user_load(12);
$author_wrapper = entity_metadata_wrapper('user', $author);
$author_wrapper->get('field_user_settings')->field_notify_reply->set(0);
$author_wrapper->save();