Guatico
Speeds for the various stages of flap retraction are calculated prior to departure. In essence, these vary according to the amount of flap used for take-off (typically about half of it) and the weight of the laden aircraft. These speeds are 'bugged' on the Air Speed Indicator (ASI). At acceleration altitude (generally 1500 ft agl, but, as already mentioned, 3000 ft at some airports and 800-1000 ft following engine failure), thrust is reduced and the nose lowered to accelerate. As each pre-set 'bug' is passed, the next stage of flap is selected, until it is 'clean'. If the speeds for an unladen aircraft were to be bugged and the aircraft was heavy, selecting, say, flaps to 'up' could result in a stall.
Using the 757 as an example, the calculated speed at which the flaps are finally selected up may vary by as much as 50 kts (58 mph), dependent purely on weight.
Oh, in case you were wondering, a 'bugs' are just little bits of moulded plastic that can be set at any position around the ASI. The generic term 'bug speed' is often used to refer to the speed that is 'bugged' as the target final approach/landing speed, which, of course, is also dependent on aircraft weight, though corrections are also applied according to windspeed, gust factor, possibility of windshear, etc.
Hope this helps.