Hmmm... this is a tricky one. We would rarely ask in that way. It all depends on the context, you have to use your judgement. I think normally we would guess the reason, and try to confirm e.g. "What, don't you agree with me?" "Sorry, did I just upset you?" If they are deep in thought, you might say something like: "I can see the cogs turning." With the idea you might snap them out of a daze and they might start to explain what they are thinking. Or maybe they just don't have anything to say right now and you should just continue talking. If you feel that maybe it's just not an interesting subject for them, then you can switch to some other topic.

Well Iris conversation is all about asking questions and getting answers. Even the question about being silent is absolutely fine. You can very well ask this question. But it's better to ask, '' why are you quiet'' ?