Once you’ve received the data, check for errors before proceeding. You may want to consider having a statistician on board to assist with data manipulation and analysis, depending on the complexity of the research question. You may also refer to the “How to Find a Researcher to Work With” section for tips.
One resource to consider is the e-Source book put out by the National Institutes of Health and Department of Health and Human Services Office of Behavioral & Social Science Research. You may find the chapter on Administrative Data Systems particularly useful in understanding use of medical care administrative data systems, data protection standards, and the advantages and disadvantages of using the data to inform research questions.