This is something that a favorite instructor of mine has stressed to me—the most difficult part of data analysis (and the part in which mistakes are most often

This is something that a favorite instructor of mine has stressed to me—the most difficult part of data analysis (and the part in which mistakes are most often made) is not choosing the correct analysis to do, nor actually performing it, but rather manipulating the data into the necessary shape/format. My favorite utilities for this are Hadley Wickham's plyr and reshape (http://had.co.nz/ http://had.co.nz/) (not sure if you already use these, figured I'd drop you a hint if not)