If we go section wise, Section 143(1) is for intimation when the Assessing officer processes your return on the basis of the information given by you in the return of income.If he finds any mistake, which is apparent from record(information submitted in return), then he rectifies the income/tax claim,etc.For example, the TDS claimed in Rs. 10,000 but actually TDS available in form 26AS is Rs. 8000, then AO will raise demand for Rs. 2000 plus interest along with demand order of said amount.These orders are generally(mostly) sent through e-mails.
The one which you are talking about, must be a notice from income tax department under section 143(2) which is for taking up the case for scrutiny assessment under section 143(3).This is the notice and is delivered by post to the address of the assessee.After serivng this order, the officer scrutinise your return and all other income disclosed/undisclosed and this requires you to take help of professional CA/Advocate and you have to appear before the income tax officer.Several sittings take place and the AO asks for many documents and proofs.After his satisfaction, he passes an order under section 143(3) based on the information gathered by him from the proceedings.
Generally, big cases are taken up for scrutiny under section 143(3), based on various criterias set by the information system of the department.