I have seen some suttas where the Buddha addressed Rahula. Are there suttas which explicitly state that Rahula was the Buddha's son, or does this come from the commentary?
I am known as “Fortunate Rāhula”
because I’m accomplished in both ways:
I am the son (putto) of the Buddha (buddhassa)
and I am seer of truths.
Also, it seems logical the student in MN 61 would be the Buddha's son due to the special & very firm attention given to him in relation to such a very basic yet important teaching.
Also, I cannot recall another sutta similar to MN 147 where the deities act as follows; as though it is a very special occasion, which logically supports the view Rahula is the Buddha's biological son:
Now on that occasion many thousands of deities followed the Blessed One, thinking: “Today the Blessed One will lead the venerable Rāhula further to the destruction of the taints.”
Probably not in the Sutta-Pitaka since after joining the Order, Ven. Rahula had to address the Buddha using His formal title just like other monks, and similarly for when the Buddha spoke to Ven. Rahula. But the proof is there in the Vinaya's Mahakhandhaka where the famous rule: "one should not give the going forth to a child without the parents' permission" was based on the real story of the Buddha allowing his son Rahula to join the Order when he was a child. King Suddhodana, the Buddha's father and Rahula's grandfather then expressed his concern about the incident which eventually led to the establishment of the new rule.