One of the recurring themes of this course is that we should never throw away or disregard data. (Albeit, so long as it was obtained under sound circumstances. If your definition of data for RT-PCR is making up numbers for Ct values those should probably go out the window.) We fought hard to get that data, and it tells an important story. While there is always a degree of expected variance in the data, sometimes it goes above and beyond, and we have perceived statistical outliers.
While my project focuses on the use of human and mouse cell culture, my lab as a whole utilizes mice as a model system to study voltage-gated sodium channels in various forms of epilepsy. We typically put transgenic mice through a pipeline of sorts, starting with behavioral paradigms and culminating in seizure paradigms. By using seizure paradigms like 6 Hz (i.e. electroshock mice to induce a seizure) or flurothyl (chemically induce a seizure), we can easily determine whether a mouse is seizure resistant or susceptible. The tricky bit is at the beginning, when we do behavioral paradigms to see if they're hyperactive, anxious, or have poor learning and memory compared to a control animal (maybe one that does not carry a sodium channel mutation). Mice inherently are variable in terms of behavior; some are more active than others, some are more lethargic. But this inherent variability makes it really difficult to determine any differences in behavior, because in a single population you have one mouse that is bouncing off walls whereas some just stay in a corner of a box the entire time. We often put mice through multiple paradigms testing the same trait (let's say, anxiety, in this case) to make sure any findings are consistent, and then Grubb the data through GraphPad to pinpoint any outliers.
That being said, what would be the best thing to do if we find an outlier mouse for one anxiety paradigm, but not for the others? Let's say, in each of the following paradigms, Mouse A is:
Paradigm 1: Not an outlier
Paradigm 2: Outlier
Paradigm 3: Not an outlier
Paradigm 4: Not an outlier
There are two options that I can see. The first is to denote Mouse A as an outlier in Paradigm 2 alone, since that's what the Grubb test told us. We would not remove it from our published data sets or from statistical analyses, but we would label it as an outlier on graphs. The second is to mark Mouse A as an outlier in each of the four paradigms, since they all measure anxiety, and it was anxious in one of them. Is that the right thing to do? Is even considering the mouse in these data sets if Grubbs labeled it as an outlier the right thing to do (well, yes, but it's still debated)? One could argue that since these paradigms test anxiety in different settings, the results from one are self-contained, meaning that Mouse A may just not respond well to a particular test, but the other camp also has a valid argument in that it's fishy if Mouse A is "abnormal" in Paradigm 2 but we still consider it as within the sample population for the other paradigms.
Perhaps it's best to just follow the literature and precedent from other mouse papers, but just because something is precedent does not mean it is necessarily correct.