Hello Annette,

Unfortunately, the factors seem weird to us and not at all what we might have 
predicted in our scenario.
Does someone with more factor analysis knowledge have some suggestions for us?

I agree with what has been said before.

You must be aware that a multinormal distribution hypothesis on the responses is at the core of factor analysis, and determines the estimation process. This assumption is clearly not suited for dichotomous data. I also seriously doubt that changing the number of factors selection criterion will be of much help with that.

The way to go for you is Item Response Theory. You should try a Rasch model in the first place (try the eRm library in R).

Best regards,

Yvonnick Noel
University of Brittany, Rennes
France


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