Hi everybody, I need some help with an analysis of pupillometric data; it’s the first time that I use pupillometry, so I hope I didn’t make too many mistakes or at least that they won’t jeopardize the whole analysis.

I ran a between-subjects experiment in which the participants watched the same visual stimulus in three different conditions; during the stimulus presentation I recorded their eye-tracking data. I'm very interested in pupillometry but here's my problem:

  • the software I use (iMotions) provides me with the aggregated and auto-scaled data for each of the three conditions: these data are apparently very clean and consistent (there has to be some kind of automated correction of blinks and artifacts).
  • The software output basically has two columns: timestamp (in milliseconds, identical in the three conditions) and pupil diameter (in cm, strangely enough, but never mind…)
  • I ran an ANOVA with the condition as the factor and the pupil diameter as the dependent. variable, F(2, 5141) = 119.38, p < .001 ηp2 = .044, (1-β) > .99. Bonferroni corrected post-hocs were all significant p < .001 (see graph 1 in attachment)
  • I got suspicious: the significance was too high and, above all, the three conditions do not start at the same point on the y axis (ycond1 = 0.47; ycond2 = 0.47; ycond3 = 0.50). I thought that maybe the significant difference could be due to this (let’s say the participants in Condition 3 had larger pupils for some reason); so, to baseline the data, I tried to let them start at the same point.
  • To do this, I rearranged the columns for them to show me not the pupil diameter but the pupil dilation; I organized them so that the new y value of, let’s say, x = 1 (time frame = 132) was the old y value (pupil diameter) minus the value of y with x = 0) (see attached screenshot) In the example, for condition 1; the new value for timeframe 132 is: 0,48 - 0,47 = 0,01.
  • I ran the same ANOVA and now the results appear to be more reliable, F(2, 5141) = 42.15, p < .001 ηp2 = .016, (1-β) > .99. There has been a drastic decrease in the F value and partial eta squared. Bonferroni corrected post-hoc analyses revealed that the condition 2 only was significantly different from the other ones (p < .001) (see graph 2).
  • …and now…question time!

  • Would you say that this procedure is right? I guess there could be many errors in it, but I’m not an expert and I didn’t manage to take great advantage from reading many papers on this matter.
  • Would you have trusted the ANOVA results at point 3? Or rather I was right to baseline those data?
  • To baseline the data, I acted freely and according to nothing but a rule of thumb that came into my mind. Would you suggest other processes?
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