This topic explains how to interpret the colours and flash sequence of the main LED. Some of the LED patterns have associated sound/tone patterns as listed in Sounds (Pixhawk).
Flashing red and blue: Initializing gyroscopes. Hold the vehicle still and level while it initializes the sensors.
Flashing blue: Disarmed, no GPS lock found. Autopilot, loiter and return-to-launch modes require GPS lock.
Solid blue: Armed with no GPS lock
Flashing green: Disarmed (ready to arm), GPS lock acquired. Quick double tone when disarming from the armed state.
Fast Flashing green: Same as above but GPS is using SBAS (so should have better position estimate).
Solid green - with single long tone at time of arming: Armed, GPS lock acquired. Ready to fly!
Double flashing yellow: Failing pre-arm checks (system refuses to arm).
Single Flashing yellow: Radio failsafe activated
Flashing yellow - with quick beeping tone: Battery failsafe activated
Flashing yellow and blue - with high-high-high-low tone sequence (dah-dah-dah-doh): GPS glitch or GPS failsafe activated
Flashing red and yellow - with rising tone: EKF or Inertial Nav failure
Flashing purple and yellow: Barometer glitch
Solid Red: Error
Solid Red with `SOS tone sequence <http://firmware.ardupilot.org/downloads/wiki/pixhawk_sound_files/NoSDCard_short.wav>`__: SD Card missing (or other SD error like bad format etc.)