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I am applying for a PhD and I am asked for 3 recommendation letters. I have 2 which I think are good letters. I am looking for someone to provide the third. I had 4 courses with a certain professor in my undergrad. I scored B+ (3.25/4) in two courses and an A (3.75/4) in the other two. Long story short, I know and the professor knows that I deserve a much higher grade in the two courses which I scored B+ in. I am thinking of asking him for his reference letter as I think they might help in making the effect of these two B+s less sever. I think I have gained a lot of respect from him in last year or two which made me think that his recommendation might be positive, but I am not sure about what he will write.

Is it logical to ask him or should I ask someone else ? I don't have many other option; The other professors only taught me one or two courses and I am not sure if I can get good recommendations from them. Additionally, that professor was at the committee for my final project presentation in my undergrad. I scored very high in that too.

I am little confused on which is better, a recommendation from this professor, or from a professor who taught me one course and I scored an A+, or from a professional referee since my other two referees are academics.

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    The one that is best is the one that knows you best and is most confident that you're a good Ph.D. candidate in your field. The company isn't going to look closely at who taught which class; they will look closely at the qualifications of the person writing the recommendation and what they have to say about you. Your belief that the professor believes you could/should have been scored higher is a fragile bridge to walk on; if you don't KNOW that he will give you a strong recommendation despite your grades, he wouldn't be my first choice. – keshlam Sep 14 '14 at 2:20
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    It is perfectly fine to ask a professor if he thinks he can give you a strong recommendation. – Greg Sep 14 '14 at 16:14
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If they were genuinely bad grades, I would advise against using this professor. But a B+ is not "really" a bad grade, even though you might have done better.

Some professors are stricter than average, and a B+ from them is the equivalent of an A- or even an A from most others. This could well be the case here. One of my friends was told that he was in the "top 5" of his class. But there were only two A's, which explains his B+. If this is the case with you, this professor is in the best position to vouch for the quality of your work, and the fact that it would be worth an A elsewhere.

In your shoes, I would schedule a meeting with the professor to find out how he feels about your work, and about recommending you. It could be that you were one of his best students that he'd recommend above most others (one student on another post reported being the "best student" in a class where he got the highest grade, 90%). On the other hand, he may think that you are "nothing special" in which case you should go another way.

Up to now, everything I've written is "speculation," so you need to find out what the "facts" are before making a decision.

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