Evaluation of cell migration data

#1
I have data from a cell migration assay that I need to evaluate statistically. I have a number of replicates for each condition and the total number (#) of migrated cells for each replicate and condition (control vs treatment with different substances).

The scientific question is: Is there a significant difference between the control (= untreated cells) and the experimental set-ups where the cells were treated with substance 1 or substance 2?

Now, there are various ways of evaluating the data. I could do the following type of comparisons:
* total # of migrated cells under the different conditions
* % of migrated cells relative to total # of seeded cells
* % increase in # of migrated cells vs control mean
* fold change of # of migrated cells vs control mean

Depending on which data sets I use, I would get different results from the statistical analysis. So, I wonder: Which type of evaluation would be best for the statistical analysis and why?