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I recently defended my PhD thesis and was awarded a pass with some minor corrections. I am due to submit the final version of my thesis very soon.

The examiners were both very happy with my thesis, which explains the final verdict. However, as the saying goes, no one understands a thesis better than its author, as the person was invested in it for years. When polishing the papers to send for publication, my supervisor and I found a major issue with the thesis, which although it does not invalidate the overall findings, it would change a significant portion of the methodology in my thesis. While I am currently addressing these issues for the publication of one of the chapters, as well as my job market paper, this issue has to led to severe depression and has made me feel inadequate as a researcher. I worked incredibly hard and had a particularly difficult PhD process; so it is difficult for me to find that at this stage (post defense) I am submitting a thesis that is predicated on a methodology that should have been approached entirely differently; and frankly while in my corrections, I have in essence remedied the problem so that it fits my analysis, changing it as I had intended it to would imply changing a substantial portion of the thesis. This in turn has caused a feeling of despair and inadequacy.

I spoke to a friend who is currently working as an associate professor and he comforted me by saying that irreproducibility, inaccuracies, and mistakes, be it major or minor are very common in vast majority of PhD theses and that I should not beat myself up for this and that the said PhD title is well deserved. However, I thought I ask for some second opinion.

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    @AnonymousPhysicist I don't think that is the same question at all. It may be related to the answer though. – 6005 May 20 '20 at 13:26
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    Shortcomings are normal in that vast majority of theses. - Inaccuracies: Depends. Quickly reading through your post it may cause future problems, but you may equally overthink it. - Your advisor of the university is possibly the better person to ask. Maybe you can add a note/an extension that details some of the problems if you have no means to correct them? – DetlevCM May 20 '20 at 19:52
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    You have a set of highly qualified folks happy with your work. Please feel free to not be less than completely satisfied with it yourself - but don't let that slow down your moving on to better things. And honestly you really should move on to the next steps given the negative psychological effects. While you prepare for your next career steps you might want to prioritize your own health and not a perfect corrected/updated version of the thesis. – StephenBoesch May 20 '20 at 21:45
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    Is It OK To Have A PhD Thesis With Shortcomings And Inaccuracies? — As opposed to what? – JeffE May 21 '20 at 17:08
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    One of the most cited senior researchers in my field once said: "I've never finished my PhD. Of course, I submitted the thesis someday, but I am still working on it." - in his 60's. – oekopez May 22 '20 at 11:43
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The thesis is a "good" one if you have passed and will be awarded your degree. Don't overthink it. You have learned something from producing it that you can leverage into future work. That is, in lots of ways, a big advantage. If your advisor is also happy and wants to work with you on any future extension, you have a positive outcome, if not a perfect one.

That the thesis "might have been better, if only..." is true pretty frequently.

My suggestion is to take the advice of the reviewers and get done. Then write a future paper extending and improving on the thesis. Don't make it harder than it needs to be. Your dissertation shouldn't be thought of as your life's best work, only its first.

Don't let the perfect be the enemy of the good. (apologies to Voltaire)

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    I think this is an amazing answer. Wow. – Coder May 20 '20 at 21:18
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    I wanted to answer just that, with an emphasis on writing a paper afterwards to solve issues in your thesis. Your thesis was accepted, with its shortcomings. Science moves ahead among others by fixing these shortcomings. – WoJ May 21 '20 at 11:38
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    Top Answer! People forget that a PhD is a 'learning degree'. Too often, completion is treated as the end, when really it is only just the beginning. If you learned something and can express that you know how or why errors occurred and what they mean for your work, then you have proved you justify being awarded your PhD. A PhD is about the process, not the end result. – Nathan Thomas May 21 '20 at 21:23
  • This Q + A was so good I shared it to my colleagues. – GrayLiterature May 22 '20 at 15:44
  • "might have been better, if only..." is true for most published research. The predicate can almost always be filled in with "if only...we had more time and funding". – lfalin May 22 '20 at 18:54
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Even if it is hard to consider when you are doing/have just completed your PhD, the thesis is not your magnum opus, but rather less-than-perfect showcase of your skills that was assessed as good enough by your peers to consider you as an autonomous researcher.

In a way, I would say that it is closer to a swimming certificate that proves that you can now swim by yourself in the deep end.

It doesn't mean that your technique is perfect, nor that you are an Olympic athlete. It only means you can now be considered as an autonomous junior swimmer that knows the basics, but of course will still benefit from guidance from experienced swimmers to get better and perfect its technique.

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Almost all PhD students go through a phase right before their viva where they realise that the entire thesis is wrong and there is a significant, fundamental problem that brings everything down. That is rarely the case and it is quite possible you fall into that category. It is more common that the thesis has already known weaknesses in the form of incomplete parts that are not theoretically or empirically tightproof. To some degree, that happens in all theses. All of them have some sort of problem, shadow or error, although not to the point that the entire work is invalidated. There are also the cases of famous academics where they discovered years later that their work was all wrong or had been done decades ago by someone else but was forgotten in the meantime.

If there is indeed a problem and the examiners have not given you corrections on it, you have no reason to alter your thesis or spend an indefinite amount of time to improve it on your own. That would be dangerous. If you find that dishonest, you can add a paragraph explaining the potential issue that requires further research. You can then wrap up your thesis and turn this real or perceived issue into a new research question, which will give you a new paper.

(Not that this is the case with you, but I remember this time when I was reading a thesis from a world famous university only to realise that most of the equations were wrong. Fun times.)

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Yes it's OK. For example, the PhD thesis of Dedekind was actually rather average (not saying that yours is) and showed no signs of his future achievements in mathematics. Everyone develops differently anyway.

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In addition to @Titus and @Buffy answers, consider describing the known shortcoming(s) in Threats to the validity section of your thesis.

There is nothing wrong to have shortcomings or limitations. Explain the shortcomings and motivate why your results are still good enough.

By being upfront, you shield yourself from the potential critique that you have misled your reviewers and readers.

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This is regarded as point of reference as most of the topic will be in detailed explanation of the fact. Some error and shortcoming of your own findings is almost normal for 95% of cases. It should not involve any misinterpretation of the facts. We can substantiate with new finding and negate almost all shortcoming in your future work will be the best attempt. All might not be in your hand or in your capacity to do, so justify it to you some other means whatever you feel satisfy you. Do not depress, world is not perfect.

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Is it really possible to have a thesis without shortcomings and inaccuracies? In all, it is a human product. With your thesis, you put forward/test an hypothesis, a premise or statement, and that should be defendable given the work you have done. But it is never perfect and always open to interpretation and opinion.

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If you kept correcting everything you found wrong in your thesis you would literally be revising it for the rest of your life.

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