Hi, my name is Andreas Fromkorth and I am a statistician at Stegmann Systems. One of my tasks is the project management for the development of new document types in PLA. The most important and also most complex document type in PLA is the Quantitative Response Assay document type. To make it a little easier to get started, I would like to explain here what you have to do to create and calculate a new Quantitative Response Assay step by step. From the new document to the finished PDF report of the calculated assay.
Step 1: Create a new Quantitative Response Assay document.
To create a new Quantitative Response Assay just right-click in the navigator on the folder, where the assays should be stored and select "New...". The appearing dialogue allows you to select the document type or the template, that should be created. For creating a new Quantitative Response Assay document please select "New Quantitative Response Assay" and press "Create".
After a few seconds the content view of the new document is shown on the screen.
Step 2: Enter the document name
Even if this is not absolutely necessary, a meaningful document name should be assigned before the first saving. This simplifies later retrieval of the document. So enter the document title in the "Name" element. For my demo document I enter the name "My 1st assay". This name is shown in the navigator panel after saving.
Step 3: Define the assay elements
Now it is time to define the assay elements for our assay. By default, a standard sample and a test sample are already created here. Select the element "Assay Element" in the outline and click on "Expand" in the top right section of the screen. The content view of your document should now look like the following picture.
Now we create an additional test sample by double-clicking on "Test Sample" in the "Creatable Elements" section on the right hand side of the screen. Now an additional test sample with name "UNK2" is created. The rest of this step is for information only. If you want to continue quickly, you can simply go to the next step.
The most important subelements of every assay element definition block are the elements "Name", "Preparation Scheme" and "Data Selection Scheme". "Name" is the name of the "Assay Element". The element name can be easily changed by the user. For example, you can simply name the standard sample "Reference". The elements "Preparation Scheme" and "Data Selection Scheme" are slightly more interesting. A scheme defined in the sections "Preparation Schemes" and "Data Selection Schemes" can be selected here. Preparation schemes define, for example, the dose sequence. Data selection schemes enable, among other things, the activation of outlier detection. By pressing "Shift" and clicking with the left mouse button on the link, you directly get to the referenced scheme.
Step 4: Preparation Scheme Setup
Without changing the preparation scheme, every sample has 2 dosis steps with 1 replicate by using a 2-fold sequence starting with 1. To make it a little bit more complex, we change this to a 3 step sequence, i.e. our in-plate dose values will be 1, 0.5 and 0.25. To do this, we select the element "Preparation Schemes" in the outline and press on "Expand". Now change the value of the element "Step Count" from 2 to 3 and the value of "Replicate Count" from 1 to 2. The conent view of the document should now look like
Step 5: Defining a Test System
One of the strengths of PLA is certainly the ability to easily define complex suitability test systems. In our example, we define a test system as proposed in the European Pharmacopoeia. To do this please select the element "Sample Suitability Tests" in the outline and add three times the element "F-Test (Hypothesis Test)" by double-clicking on the corresponding element in the "Creatable Elements" section. You might note, that you now have three F-Test (Hypothesis Test) elements with the test type "Significance of Non-Parallelism". Please change the test type of one of the tests to "Significance of Regression" and the test type of another test to "Significance of Non-Linearity (Lack of Fit)".
Step 6: Acquisition of measurement data
Before the actual data collection can begin, the data table must first be prefilled. However, this is very simple when using the "Assignments" functionality. To do this please select the button "Observations" in the editors side bar.
And now select "Assignments" ? "Sequence" ? "Observation Group ID" -> "Sequence Step". With the exception of the "Reponse" column, all data columns are now prefilled based on the information in the assay element definitions and the respective "Preparation Scheme".
For the daily work we recommend to use one of the numerous PLA "Data Acquisition" modules at this point. Here, however, we will now record the measurement data manually.
The fastest way doing this is opening the file "assay data.txt" with a text editor, copy the whole content of the file and paste it into the response column. To do this, select the first cell of the Response column and press Ctrl-V after copying the conent of the "assay data.txt" into the clipboard. In most editors you can do this by pressing Ctrl-A and then Ctrl-C.
Step 7: Save the document
Now we save the document. One way doing this is pressing Ctrl-S.
Step 8: Calculate the assay
To calculate the assay, click on the 'Calculate' button in the editor side bar. Now a dialogue appears showing the calculation progress. Please note, that the first calculation after log-in always takes a little bit longer, because of the starting procedure of the calculation engine. After starting the engine, a calculation will be much faster. After finishing the calculation please close the 'Calculation Dialogue', if this is not done automatically.
Step 9: Generate a report
Now we can create a report of the assay. Klick on "Report...", select the Detailed Report and click on "Start". Now a pdf report of the assay is generated and automatically opened in your default pdf viewer.
Of course, there are a lot of more option available in the Quantitative Response Assay document. For example you can choose another regression model in the Analysis section, define complex test systems by adding additional suitability tests or use an assay control.