Rectified e return u/s 139(1) or u/s 139(4) ?

i had filed my it return for AY 2011-12 online before due date & return is showing refund

there was a difference of amount  of TDS which was shown on my form no 16 & amount entered online

due to this CPC had send me anotice to pay income tax of more then 15,000 u/s 143(1)

After checking  the data with my employer there was an error in entering the TDS on their part

this metter is corrected & it can be seen on NSDL website

now i have to file rectified e return

under which section i should file it ? u/s 139(1) or u/s 139(4)