Tune the initial attack.

If you play the guitar, you may notice that after you pluck a string the meter will slowly move flat as the sound decays. This is due to the the average string tension being higher the harder it oscillates. You may not notice this on other tuners, since they do not have a high enough resolution to show the pitch difference. For a proper tune you must tune the initial attack using a moderate pick pressure, then let the reading settle slightly flat.

Don't tune in extreme temperatures.

The oscillator used to measure time in the iPhone can be slightly affected by extreme temperatures. This is common to all tuners aside from expensive temperature compensated models. The effect is very slight (about 3 cents sharp at 104ºF / 40ºC, which is still more accurate than many other tuners), but be aware that your accuracy may be slightly affected at extreme temperatures.

Turn Needle Damping on for decreased response time

If you play a woodwind or brass instrument, you may notice that the needle oscillates slightly back and forth. This is because Cleartune is actually tracking the slight vibrato of your breath. (If you move your iPhone/iPod toward and away from a constant tone, you will notice it actually tracks the Doppler Effect). Turn the Needle Damping option on to filter out periodic fluctuations like this so you don't get dizzy.

Temperaments

If you're not sure what temperaments are, you should most likely keep it set on Equal Temperament. If you play guitar, setting the PowerTonal™ Guitar temperament will slightly adjust the pitches of the first few strings (and the octave E) in order to bring the fifths typical in "power chords" more in harmony. You can use this setting if you tune to a standard EADGBE or half step drop tuning.

Transposition

This setting should be left at C unless you play a transposing instrument such as the Bb trumpet or Eb saxophone. If you play a transposing instrument, set this setting to the key of your instrument such as Bb for Bb trumpet.