PAIRED DIFFERENCE: this is a non-parametric statistical calculation. There is no need for SPSS or any software. See attached if use SPSS. You can do it by hand or Excel. You have two series that are produced by two stimuli. You want to compare their difference and answer the question: Whether the reading from different dosage have statistical significance?
Td = d^ / [Sd / sqrt(n)]
where d = difference of the paired reading for corresponding time (ti1 : tj1), (ti2 : tj2), ...etc., d^ = mean of the difference, i.e. d = (di - dj), Sd = standard deviation of di series, and n = sample size; here n = 5. The decision rule for 95% at degree of freedom df = n - 1 or df = 4, the critical value given by the T table is 2.13.
H(0): Td < 2.13
H(A): Td > 2.13
The result of the first batch of data shows Td(obs) = 1.82 and the second batch is Td = 1.42. In both cases, the null hypothesis cannot be rejected. We conclude that there is no significant difference among the reading produced by dose 1 and dose.
REFERENCE: See attached Excel and PDF. Also download: http://www.statstutor.ac.uk/resources/uploaded/paired-t-test.pdf
Your question is not clear. What do you mean by analyzing the difference between two dependent variables? If you mean the difference between the means of two dependent variables then Paul gave you the answer and you can use the matched two sample t-test in SPSS. If you want to compare the behavior of two series of time-related observations then you can use cross-correlation between two series. However, if you want to compare the distributions of the two variables you can use KS test. Please specify what you need..