It's necessary to account for the complex survey design when analyzing MEPS data so that standard errors are estimated correctly and valid design-based inferences are obtained.
The following link provides basic examples of programming code for five statistical software packages that are commonly used to analyze complex survey data. Examples are applied to MEPS 2011 data.
Using Statistical Software Packages to Produce Estimates from MEPS Data Files
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The following link addresses common questions regarding the need to account for the lack of statistical independence among observations when analyzing MEPS data.
Accounting for Clustering in the Analysis of MEPS Data: Frequently Asked Questions
(PDF, 286 KB)