No, you cannot complete a full two-way ANOVA if you are missing one level of samples after data collection. A two-way ANOVA relies on having data for all combinations of the two independent variables.
Here's why it's problematic:
Missing Cell: With a missing level, you wouldn't have data for one of the cells in the ANOVA table. This creates an incomplete picture of the interaction between the two factors.
Degrees of Freedom: The number of degrees of freedom (DF) used to calculate the F-statistic in ANOVA depends on the number of cells in the table. Missing a level reduces the DF, making it difficult to assess the significance of the effects. @Melton r. Harvey
A two-way ANOVA analysis, it is imperative to have complete data for all levels of the independent variables in order to accurately assess the main effects and interactions. If one level of samples is missing after data collection, this poses a significant challenge as it can lead to biased results and jeopardize the validity of the statistical analysis. In such cases, researchers must carefully consider how to address the missing data, whether through imputation techniques or excluding incomplete cases from the analysis. Imputation methods such as mean substitution or regression-based imputation may be used to estimate missing values; however, these approaches come with their own set of assumptions and limitations which should be taken into consideration when interpreting the results. It is crucial for researchers to transparently report any missing data issues in their findings and justify their chosen method of handling the missing level in order to maintain rigor and credibility in their research approach.