Good data management can make the process of analysis much easier, so let's recap some of the tips from earlier phases.
Take snapshots of your data at these key points, at least. A snapshot is just a locked copy of your data files, saved to a backup storage location. These files should not be changed; they are for reference only. That means you make a copy of the file for editing or before moving on to the next phase (and be sure to rename it!).
During the analysis process, help yourself by taking good notes and clearly versioning your analysis scripts and files