EMBRAER 145 JET FLC TOOK OFF WITHOUT CLRNC DUE TO A MISUNDERSTANDING OF TWR CLRNC WHILE IN POS AND HOLDING.

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WE WERE CLRED INTO POS ON RWY 29 IN EWR AND COMPLETED THE BEFORE TKOF CHKLIST TO THE LINE. WE WERE EXPECTING TO FLY THE EWR RWY 7 SID (265 DEGS; 5000 FT). AS ANOTHER ACFT WAS LNDG ON RWY 22L; ATC SAID 'FLY RWY HEADING; MAINTAIN 2000 FT;' AND WE COMMENCED THE TKOF. A FEW HUNDRED FEET INTO THE AIR; ATC SAID THAT WE HAD NOT BEEN CLRED FOR TKOF AND TO LOOK FOR A HELI AHEAD. WE SAW IT AND DID NOT NEED TO CHANGE OUR FLT PATH AND THERE WAS NO TA OR RA. I TOLD ATC WHAT I HAD HEARD AS THE TKOF CLRNC; BUT HE REPEATED THAT WE WEREN'T CLRED. BOTH THE FO AND I WERE STUNNED BY THIS. EVERYTHING WAS IN PLACE FOR OUR DEP. THE XING TFC LANDED; THE RWY WAS CLR AND ATC GAVE US INSTRUCTIONS CONSISTENT WITH A TKOF CLRNC. NORMALLY; IF ATC HAD ALTERNATE INSTRUCTIONS; BUT NOT A CLRNC; THEY ARE VERY CLR ABOUT CONTINUING TO HOLD. OUR INSTRUCTIONS WERE TYPICAL OF A CHANGE IN DEP PLANS THAT ARE FOLLOWED BY A TKOF CLRNC. UPON ARR AT DEST; WE BRIEFED OUR CHIEF PLT. I WAS ASKED TO CALL EWR TWR AND THE SUPVR ASKED ME FOR MY CONTACT INFO AND SAID THERE WAS GOING TO BE AN INVESTIGATION. SHORTLY THEREAFTER; I RECEIVED A CALL; BUT LET IT GO TO VOICEMAIL AND IT WAS THE TWR CALLING ME. BEFORE I CALLED BACK; I ADVISED MY CHIEF PLT THAT I HAD ORIGINALLY PLANNED TO TAKE A NAP DURING MY 2 HR BREAK; BUT SINCE I WAS TIED UP WITH THIS EVENT; I WOULD NEED TO BE RELIEVED OF MY LAST TURN DUE TO FATIGUE. I HAD A REDUCED REST 2 NIGHTS AGO (5.5 HRS OF SLEEP) AND AN XA30 AM WAKEUP CALL THIS MORNING (5-6 HRS OF SLEEP). I FIGURED I HAD ENOUGH FOR 1 DAY AND THAT IT WASN'T SAFE TO FLY THE LAST TURN GIVEN THE LACK OF SLEEP AND THE STRESS OF A POSSIBLE CERTIFICATE ACTION. WHILE I BELIEVE THE OVERWHELMING REASON WE COMMENCED THE TKOF WAS DUE TO THE TIMING AND NATURE OF ATC'S XMISSION; THE LACK OF SLEEP CERTAINLY DIMINISHED MY ALERTNESS; BUT NOT TO A DEGREE THAT I FELT AT RISK AS THE WX WAS CLR. I TAKE EXTRA DILIGENCE AND CARE WHEN LACKING A FULL NIGHT'S SLEEP. I RETURNED THE CALL TO THE EWR TWR ABOUT 1 HR AFTER RECEIVING THE VOICEMAIL. I WAS TOLD THAT AFTER REVIEW OF THE TAPE; THE AMBIGUITY WAS APPARENT AND THAT NO FURTHER ACTION WOULD BE TAKEN. I WAS ADVISED TO BE MORE ALERT TO THE SPECIFIC 'CLRED FOR TKOF' CLRNC AND THE CTLR THAT WORKED MY FLT WAS ADVISED TO REITERATE THE 'POS AND HOLD' INSTRUCTION NEXT TIME. WHEN A CREW TAKES THE RWY; THERE IS THE ANTICIPATION OF AN IMMINENT DEP. THE ISSUANCE OF ALTERNATE TKOF INSTRUCTIONS WITHOUT A TKOF CLRNC IS TO A DEGREE ABNORMAL AND UNEXPECTED AND I BELIEVE CTLRS SHOULD BE EXTRA CAUTIOUS BY REITERATING THE CURRENT 'POS AND HOLD' CLRNC. THIS EVENT CERTAINLY GOT MY ATTN; AND I'LL BE EVEN MORE DILIGENT IN THE FUTURE. ALSO; ATC AT EWR WAS VERY PROFESSIONAL DURING THE EVENT AND ON THE PHONE AS WELL.