I assume you are talking about FID responses of N and O containing compounds. As a rule of thumb the FID response is proportional to the carbon content of the compound. Thus an aromatic hydrocarbon such as toluene (91% C) has approximately 2.5 times the FID response of an O-containing compound of similar MW such as ethyl acetate (54.5% C). N- and O-containing compounds with the same %C content will have a similar FID responses.
I suspect you may be comparing compounds with a single N with a those containing multiple O atoms or the MWs of the N-containing molecules are much higher than those of the O-containing molecules which has a big effect on the %C content.