In which subject should I do Ph.D after completing MCA in 2007 and with Experience in Marketing? Which is best University for me?

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If premier institutes like IISc / IIt/ IIIT etc offers Phd in Computer Science in Distance Education, Then no problem in going for that.

But always its better to do PhD in full time as this is the exit degree and highest degree of its kind available in India.

You have decide on your career path. For this you have to take decision whether the same should your academic knowledge or work experience. Once you take a decision you need to check out the institutes offering this specialisation. You also need to decide on whether you would like to pursue the same in the country or abroad. Check out the admission procedure of the same. Normally there will be a requirement to clear the entrance exam. The questions will be related to field you plan to pursue. There can be questions related to the aptitude too. You will get all the details in the website of the institute where you plan to pursue PH.d.