Youden Square Design (YSD) is an incomplete latin square design with at least one row/column which can’t run in an experiment. In this research we took 5x4 YSD (one column is not runned in an experiment). This design has a balance characteristic from a balanced incomplete block design where all treatments appears with the same number in each row. Missing data can occur in YSD. In this discussion, YSD with two missing data was used. Missing data is estimated by an iterative method then we arrange analysis of variance and LSD test. Analysis of variance with two missing data in YSD is calculated by adjusting the treatment sum of squares with it’s bias value and the total degrees of freedom and error degrees of freedom are substracted by two. LSD test is carried out if the treatment has a significant effect to the response. To clarify the discussion in YSD, example of application in the field of industry is given by observing the effect of the assembly method to the length of assembly time of X component. The assembly method has an effect to the length of assembly time of X component and if the missing data are and so the suggested assembly method is E method because it has the fastest average assembly time. Keywords: YSD, Missing Data, Analysis of Variance, LSD Test
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