A quasi-replicate is a factor whose levels are not included in the design calculation, but rather define how many times the entire design is replicated for each of its factor levels.
For example, if in your experiment you have cells from three different donors, and you want to calculate the variability across the different donor sources of cells, you may wish to replicate your entire design three times, based on the factor ‘Donor Cells’.
In Synthace, any factor specified that is mapped to an element parameter or a Custom Factor can be a quasi-replicate factor.
When calculating a design where more than one quasi-replicate factor is defined, the levels for each quasi-replicate are not treated in the same way as ordinary design factors (i.e., various different combinations of the factors and their levels). Instead, with quasi-replicate factors, the levels of one factor are matched to the levels of the next quasi-replicate factor in the order they are defined.
For example, if I define two quasi replicate-factors, QR1 and QR2, with levels 1 and 2, and A and B, respectively, my design will be replicated twice, once with a treatment of 1 and A, and a second time with a treatment of 2 and B. As such every quasi-replicate factor must have the same number of levels defined.
In this tutorial you will learn:
How to define more than one factor as a Quasi-Replicate.
Defining quasi-replicate factors
Follow this tutorial to learn how to define a single quasi-replicate factor, then continue with the following steps.
Add a new categorical factor to the Custom Factors section called Antibody with the levels A, B and C. For more detail on how to do this, click here.
Click on the quasi-replicate check box before adding the factor to the factor table.
Note: In any factor that you set up in Synthace you have the option to treat it as a Quasi-Replicate factor by checking this box.
Check the Quasi-Replicates
Click on the Calculate Design tab at the top of the Factor Table.
Note: Quasi-Replicate factors are not included in the power calculations. They do not contribute to the actual design, but replicate the design the same number of times as the number of levels in the quasi-replicate factors.
Scroll to the Design Matrix at the bottom of the panel.
Note: While the calculated design only has 96 runs, you will notice that you require 288 runs in total - 96 runs for each of the three Donor Cell types and Antibody combinations defined. Scrolling through the design matrix table you will see that the 96 runs are replicated 3 times, once for each Donor Cells type and Antibody combination. Donor 1 is paired with Antibody A, Donor 2 is paired with Antibody B, etc. By default, the 96 run order is replicated exactly for each quasi-replicate, however you can chose various randomisation options at the top of the page in the settings panel.
Well done on making it to the end of this tutorial.
To learn more about Quasi-replicating factors see here.
To learn about the different quasi-replicate randomisation options, click here.