B737-700 FLT CREW REPORTS CONFLICT ON TKOF ROLL WITH COMMUTER ACFT LANDING ON INTERSECTING RWY. COMMUTER ACFT IS ISSUED A GO AROUND BY THE TOWER.

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ATC CONGESTION CAUSED A 46 MIN DELAY FROM PUSH TO TKOF. AFTER BEING 'CLRED ONTO HOLD RWY 9L;' WE PROCEEDED INTO POS AND HOLD FOR APPROX 30 SECONDS BEFORE BEING 'CLRED FOR TKOF' ON RWY 9L. I MENTIONED TO THE CAPT A COMMUTER TYPE TWIN ENG ACFT ON OUR R COMING INTO RWY 35. AT THAT POINT WE RELEASED BRAKES AND SET TKOF PWR. DURING THE TKOF ROLL; THE ACFT APCHING RWY 35 WAS GIVEN A 'GAR L SIDE.' THE CAPT MADE A V1 CALL AND THEN THERE WAS A LONGER THAN ANTICIPATED DELAY IN MY MIND FOR THE ROTATE CALL. I CHKED THE AIRSPD AND STARTED TO ROTATE AFTER SEEING THE AIRSPD PAST VR. THE CAPT CALLED 'NOT YET.' I LOWERED THE NOSE BACK TO THE RWY AS WE ACCELERATED PAST ROTATION SPD AND I SAW THE COMMUTER GOING AROUND ABOVE US. AT THIS POINT HE CALLED ROTATE AND WE TOOK OFF. TWR WAS QUIET DURING OUR TKOF AND ROTATION. AFTER WE PASSED APPROX 1000 FT AGL; THE TWR TOLD US TO CONTACT PHILADELPHIA APCH. NO FURTHER COMMENTS WERE MADE BY TWR OR ATC DURING THE REST OF THE FLT. ANOTHER CARRIER DC9 HAD JUST BEEN HELD FOR TKOF FOR A SIMILAR SITUATION AHEAD OF US. THAT ACFT WAS HELD UNTIL THE ACFT APCHING RWY 35 LANDED. IN OUR CASE; IT APPEARED THE TWR CTLR EITHER MISJUDGED THE CONFLICT AND PLANNED FOR US TO BE CLR BEFORE THE ARRIVING ACFT; AND WHEN HE REALIZED IT LOOKED LIKE A CONFLICT; HE TOLD THE ACFT ON APCH TO GAR VERSUS ABORTING US. THIS APPEARS TO BE A HUMAN ERROR EVENT. IT HAPPENS; BUT HE SHOULD HAVE GIVEN THE GAR ACFT MORE SPECIFIC CLBING AND TURNING DIRECTIONS AND A WARNING ABOUT OUR TKOF. I'M NOT SURE THEY WERE AWARE OF OUR DEP. SUPPLEMENTAL INFO FROM ACN 742266: ON TKOF ROLL PHL RWY 9L; HAD A CLOSE RWY INCURSION WITH A LNDG COMMUTER ACFT LNDG RWY 35. HE WENT AROUND AND MANEUVERED TOWARD MY TAIL TO MINIMIZE RISKS. WE DELAYED TKOF ROTATION UNTIL CLR. ATC INTERSECTING RWY OP TRAINING AT THE PHL TWR.