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My question is regarding how to go against advice given by advisers/faculty in a professional way, specifically in applying to graduate schools (but I am interested in the general case as well). Due to my poor test scores, one of my mentors has explicitly said that I should not apply to school X and Y. However, the location of the school and research interests of the faculty align well with my preferences so I want to apply anyways (although I must agree with my adviser that my chances are slim at best). How should I let my adviser know (he is likely to be a letter-writer for me as well)?

On a related note, should I follow his advice? I don't want to "waste" time applying to a school that is a big reach for me but I also don't want to lose hope.

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    For your second question, I'm not sure you'll be able to get useful advice from this forum; the answer almost certainly relies on details that no one here could possibly know. – eykanal Oct 27 '15 at 22:36
  • Thank you, is the main question posed properly? – Kevin Sheng Oct 27 '15 at 22:37
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    I'd just say what you said "I agree that the chances are slim, but I wanna take the chance anyway. Would you please send LoR?"... – Fábio Dias Oct 27 '15 at 23:32
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    Are you sure this is not a polite way of your adviser to tell you that his letter of recommendation would not be strong enough for that school? – Bitwise Oct 28 '15 at 12:52
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For the general question: One answer lies in the question itself. Challenge the advice with respect to the advice and your advisor. That is, appreciate and acknowledge the experience of your advisor (not necessarily in words, but at least "internally").

Moreover, give some reason. "Thanks for your advice on the topic, but I would like to do... because..." I feel like "I'd like to do it anyways" is not the best reason...

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    While I agree that a strong reason would be nice, "I'd like to do it" is reason enough for me. In the end, what the advisor did was exactly that - give advice. The real decision is yours and you will deal with the consequences of that decision. I'm not saying it is the right thing to do, I ignored some sound advises from very wise people, which turned out to be right, but nevertheless I chose what I thought was right given the information I had and I'll live with it. That said, I'd recommend the OP to carefully consider the advice, and be sure of what you want to do... – Fábio Dias Oct 28 '15 at 13:29
  • @FábioDias Can you please turn your comment into an answer? – jakebeal Oct 31 '15 at 12:12
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I personally do not think that you are "challenging" your advisor's suggestion if you decide to apply to schools that s/he does not recommend. We all know that ultimately you are the one who is responsible for your own decision. From what you have described (e.g., the location and facility of the universities), it is already clear that you know what works best for you. I personally do not think this matter is that complicated. All you need to do is to email him/her (or talk to your advisor face-to-face), thank him/her for all the time and advice s/he has spent on talking to you, and then tell your advisor your decision. S/he will respect your decision and will not take this as a gesture challenging his/her knowledge--this has happened to me from time to time; my students seek advice from me and decide to take a path not recommended by me. But, I still support their decision, giving them the best of my recommendation on the reference letter.

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Be polite, yes, ... but/and there is a further issue: the credibility of your letter writer will be adversely affected by writing a letter for you to a place that significantly exceeds the strength of your record, since it may appear that they lack the judgement to have dissuaded you from applying there. Or, alternatively, they may send a custom letter acknowledging (to avoid appearing ridiculous) that other aspects of your record make you a non-starter... Well, that's not good, either.

That is, taking these "slim chances" is not reliably cost-free (nevermind the application fee).

Also, it's not really that "long-shot gambles" pay off occasionally in such scenarios, since the element of chance applies only to applicants whose record is in the right ball-park. That is, for elite-ish places there are already too many applicants with no obvious weakness in their records...

(That is, it's not just that human physiology "reduces the chances" of being able to fly under one's own power...)

In particular, your advisor may not be too happy about writing such a letter, even if they agree to do it. So your respectful disagreement carries more baggage than you might have anticipated.

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