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So you are telling me, you did not see me appear out of it ?

I know that the idiom of "You are telling me," means "I'm well aware of that..."

But if we apply the meaning to the sentence, the sentence does not make sense or at least to me, it does sound odd. In addition, if I rewrite the sentence, I would write it without the comma, not to make it confusing or "So are you telling me (that)..."

What do you think? Do you think that we can see "you are telling me" as an idiom in the sentence and we need a comma there? Thank you so much in advance.
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There would be no such confusion because the expression always stands alone and is never introduced by so.

- It's really hot today.
- You're telling me!

Do not use a comma before a that clause, even when that is omitted.

So, you're telling me [that] you did not see me appear out of it?
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Thank you, and I am totally with you, but the problem is that we can see many sentences with misuse of commas. But as a non native English speaker, it is not easy to find reasons of using commas there and I got the sentence in a text book. So do you think not only non native English speakers but also native English speakers use commas differently or wrong sometimes?
AnonymousSo do you think not only non native English speakers but also native English speakers use commas differently or wrong sometimes?
Yes, I do think that.

This site should help you with commas:

http://grammar.ccc.commnet.edu/grammar/commas.htm

But that won't solve all your problems. Really, the only way to acquire a firm, natural grasp on applying correct punctuation is to read—read, read, read, read, read. I'm sure you have some books lying around your house. Pick one up and study the writer's use of punctuation. But at all cost, avoid that textbook you mentioned, assuming that sentence originally had a comma.