The primary difference is that subtraction is an operation that is performed as part of an expression. For example.... 2X - 4
Whereas a negative sign is not an operation but associated with an individual term in the expression..... 2X + (-4)
In the first example you are subtracting two positive "things" from each other. In the second example you are adding a positive "thing" and a negative "thing" together.
You will notice that if you were to substitute a number in for X in either of these expressions, or graph them as linear equations, you would obtain the same results for both.
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