Response to notice under section 139(4)

Cannot totally deny it, but depends upon query.

You can if it was a bonafide mistake made while selecting ITR form. 

If you had filed ITR4 first, this may mean you are maintaining Books of Accounts. Subsequently, on receiving intimation u/s 139(9), if you suddenly switch ITR forms and claim that you are not in the practice of maintaining Books, then the Assessing Officer may raise numerous queries regarding the veracity of the ITR 4S Return.

Now, if you are maintaining books of accounts, inspite of which you opt for Section 44AD and file Return under Form ITR 4S, then you need to report 8% or Actual profit as per books whichever is higher.

Hence, if filing under ITR4 in the first place was a genuine mistake, then you can file ITR4S in its place, within the specified time of receiving intimation u/s 139(9).