When plotting within-subject data for condition A vs. condition B (significance tested through a t-test), should the error bars reflect standard error of the mean for each condition independently? Or should they be SE of the mean difference between A and B?
When there are more conditions for an ANOVA -- A vs. B for condition 1 and A vs. B for condition 2 -- should the error bars correspond to the SE of mean difference of A-B at 1 and then the SE of mean difference at 2?
This paper gives a way to calculate SE/CI for within-subject designs. The gist is that the subjects are normalized to reduce the between-subject contribution to the error bars and better reflect the results of a repeated measures ANOVA.
Cousineau, D. (2005). Confidence intervals in within-subject designs: A simpler solution to Loftus and Masson’s method. Tutorial in Quantitative Methods for Psychology, 1(1), 42–45. PDF