Okay, me again, still working on this analysis. So, I have four types of fruit: a, b, c and d. Initially the reference fruit was d so, after I noted the p-values and ORs with 95% CIs for a:d, b:d, and c:d, I wanted to see if a is significantly different to b and c, and if b is different to c, so I changed the fruit around so the four types would still be a, b, c and d, but the letters would designate two of the fruit differently from the first analysis (I swapped b and d around, then later swapped c and d). So, my p-value for apples vs. oranges was originally 0.0186 but when I swapped the letters around the value for oranges vs. apples was 0.0005, which is the difference between reporting a finding or not. In total I have 6 statistical tests (a:d, b:d, c:d, a:b, a:c, b:c) so I will accept significance at 0.01 instead of 0.05 (I figure the risk of a false positive with six independent tests at 1% are roughly equal to one test at 5%). I've checked the data carefully, and there appears to have been no errorwhen I changed the letters around. There are only 90 data so visually checking is quick and easy. Of course, I could just include two fruit at a time in the model and run six pairwise logistic regressions but that wouldn't explain why the values should change in a four-fruit model when I merely swap the reference levels around. Does anyone have any advice on how I might proceed, or suggestions regarding the cause of this? It seems odd to me. Many thanks Peter
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