As in, "math error" notice, many of which have nothing to do with arithmetic?  That's a good question.  I searched for an answer about this time last year, when IRS changed my client's filing status from head of household to single, even though the return had the required information.  If you answer in 60 days, they have to issue a statutory notice of deficiency.  It's important to have proof of mailing the protest.  

I'll be at my office later today and will look up what we used.  There was no response from IRS until April, when they said they needed another 60 days.  A few weeks ago my client finally received her $2,300 refund, with interest.