That $5 per square foot deduction is using the simplified method, and that rate is assuming you used the office for the entire year. If you used the office for less than a full year, you need to adjust your square feet used for the calculation. So if your home office is 300 square feet but you used it for only 6 months, you would adjust the number of square feet to 150 to make your calculation. $150 x $5/sf = $750. Every month you use the home office for at least 15 days qualifies as a "month" for purposes of determining your home office use.
Most of the times when I run the calculations for my tax clients, I find the actual expenses are much more beneficial than the simplified method. This is especially true for high rent apartments (like New York City or Boston), where the monthly rent will create a massive tax benefit when compared to the Simplified Method.
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