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Of these three possibilities, only the third involves serious misconduct, while the other two possibilities involve problems in record keeping.
Given the information you have at this point, it is premature to conclude that misconduct has taken place. A logical first step is to find out if other people were involved in acquiring data for the publication in question.
If you are unable to track down the missing data this way, you could ask your research advisor about it directly. It is more likely that this is just a record keeping problem, so avoid any questions that sound accusatory.
If you are unable to resolve the matter at this level, you should talk to a carefully chosen outside party. It is not necessarily wise to talk to fellow graduate students about the issue. It is not clear that they will have the experience or perspective to assess the situation and you may unwittingly start unfounded rumors about your lab.
You could consider talking to the department head if you think he or she is an objective third party. You could also talk to your institution’s Misconduct Policy Officer. Your institution’s research development office can provide contact information.
Finally, it is worth noting that careful record keeping can help prevent misunderstandings. If someone else was had collected the missing data, a cross-reference in the two lab notebooks would have been helpful. Similarly, if one person accumulated all of the data but the information was stored differently, that point should be noted in his or her lab book.
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