I ran 3dMVM.R on a dataset that had 1 between-subjects variable (4 levels) and 1 within subjects variable (2 levels). However, I inadvertently set the options -SC and -bsMVT, which I realize are not needed with two levels. In every other package I’ve ever used, those options would be ignored with 2 levels as they could not really be computed, and I didn’t see any errors, but is there any consequence to the analysis itself?
No need to worry. When there are only two levels for a within-subject factor, adding -SC would not have any impact because there is no sphericity issue with only one correlation.