Incomplete Two-Factor Experiment with Repeated Measurments
A data frame
In a gene expression experiment, stem cells were differentiated using a set of factors (such as media types, cell spreads etc.). These factors were collapsed into a single cell environment configurations variable. The cell lines were assays over three days. Two of the configurations were only run on the first day and the other two were assays at baseline.
To get the materials, three donors provided materials. These donors provided (almost) equal replication across the two experimental factors (day and configuration).
One of the goals of this experiment was to assess pre-specified
differences in the configuration at each time point. For example, the
differences between configurations A and B at day one is of interest.
Also, the differences between configurations C and D at each time points
were important.
Since there are missing cells in the design, it is not a complete two-way factorial. One way to analyze this experiment is to further collapse the time and configuration data into a single variable and then specify each comparison using this factor.