Handling missing data means deciding, in a principled way, what to do about the gaps in your dataset so they do not bias your results. The defensible approach starts by classifying why values are missing, then choosing a method that fits, usually some form of imputation rather than simply deleting cases. Done carelessly, missing values quietly distort every analysis in your dissertation; done well, the handling becomes a strength your committee respects.
Why the reason for missingness decides your method
Before you fix anything, you have to name the pattern. Data can be missing completely at random, where the gaps are unrelated to anything in the study; missing at random, where missingness depends on other variables you did measure; or missing not at random, where it depends on the missing value itself, such as high earners declining to report income. The pattern matters because a method that is safe under one assumption is biased under another. Stating which pattern you believe applies, and why, is the part your assessors look for first.
The diagram above is a reminder of what is at stake. Your sample is the bridge to the population, and missing values weaken that bridge by shrinking the sample and potentially skewing who remains in it. That is the same logic behind descriptive and inferential statistics: if the sample is no longer representative, the inference built on it cannot be either.
The methods, from simplest to most defensible
The crudest option is listwise deletion, dropping any case with a missing value; it is acceptable only when data are missing completely at random and losses are small, because otherwise it discards statistical power and can introduce bias. Mean substitution, replacing gaps with the variable average, is widely discouraged because it understates variance and distorts relationships. The stronger families are multiple imputation, which generates several plausible complete datasets and pools the results to reflect the uncertainty of the gaps, and maximum likelihood estimation, which uses all available data directly. These two are the methods most likely to satisfy a methodologist.
Diagnosing and documenting the gaps
Practical handling starts in your software. Tabulate how much is missing per variable and per case, and look for whether the gaps cluster, which you would catch while cleaning data in SPSS and again when reading the SPSS output. Watch the interaction with your distributional checks too: imputing values changes the shape of a variable, so re-run any test for normality after imputation rather than before. Keep a clear record of how many values were missing, the pattern you assumed, the method you chose, and the justification, because that audit trail is what makes the analysis reproducible.
Reporting your approach with confidence
In the write-up, state the extent of missingness, the assumed mechanism, the method you applied, and any sensitivity check you ran to confirm the conclusions do not hinge on it. A short, honest paragraph that says you used multiple imputation under a missing-at-random assumption and compared it against a complete-case analysis reads far better than silence. Missing data is not a flaw to hide; treated transparently, it is evidence that you understood your dataset well enough to defend it.