Discussing avoidable flaws in my work in a master's thesis I am in the final stages of M.Sc. in bioinformatics and am currently writing my thesis. While I was writing I noticed that one of the datasets I used for a major part of my project is quite problematic and may have somewhat biased the results (if it matters, the data was obtained from a published paper. A postdoc working with me on the project had reviewed the paper and suggested that it would be appropriate for our work). I do not think this is very major bias, and I can give a concrete explanation as to the source of this bias, but still there is a bias.

I am considering of referring to all of this in my thesis as part of a broader discussion of the limitations of my work.

Knowing my thesis supervisor I suspect that his reaction will be something along the lines of "why did you use this dataset in the first place? You should have looked at the data before using it." In retrospect I wouldn't have used this dataset and yes, I should have looked at the data more carefully. However, at the time I was doing this I had no prior experience with this type of analysis, and therefore did not know what types of problems to watch out for (I was also put under continuous pressure from supervisor to produce results, which did not give me much time to ensure the quality of the data, but this is a different problem). 

From my perspective, learning to identify and avoid such problems is a valuable part of my learning process, and I therefore consider it important to demonstrate this learning process in my thesis, but I don't think my supervisor will be appreciative of this, and I really fear backlash from his. To make things more complicated, we are currently writing a paper based on these results and I fear my supervisor will blame me for undermining the paper by using this dataset.

My questions therefore are:


Is it at all appropriate to use a master's thesis to demonstrate my learning process in such a way?
How do I balance between my desire to be honest and show what I have learned and between the harsh response I am likely to get?
"if it matters, the data was obtained from a published paper" -- I would say that it matters a great deal. Talk about the issue, but spin it as a strength of your research (it uncovered a bias in the existing literature -- which is one of the things that subsequent research is supposed to do) instead of a weakness that you need to be apologetic about. If anyone should feel apologetic, it should be the authors of that paper and the referees who didn't notice the problem. You should feel proud about that aspect of your work. I don't know your advisor, but I wouldn't be surprised if he is impressed by this rather than critical of it.