I agree and disagree. For a formalized study of the differences between the two I would say yes. But I was mostly suggesting a simple pattern seeking "once over" of his history to start. Deepbit solves around 75-90 blocks a day depending on its luck, which is a sizable number to work with. He is thinking he sees ~10% difference between the two miners, which is a significant difference. Were he to look at all the points from each he should see a significant and consistent shift upward between the two data sets. As well as a significantly different average once outliers are thrown away.
To really get into the meat of the matter though I agree you need to go big on your datapoints.