Export a Graph Pad Prism file directly from OMIQ and create a XY plot. The example we give below is for a classic EC50 assay to measure drug candidate potency. The intensity or percentage of a fluorescent marker is measured over a serial dilution of the compound(s) of interest.
1. Add Metadata to your Dataset
Add any metadata that is needed to build your XY plot. For this example, X-axis (concentration), groups (drug) and replicates (repeat).
You can find out how to add metadata to your datasets here.
2. Build your Workflow
Shown above is just a example (note that the fcs files were already compensated). Build your workflow in whatever way makes sense for the data you wish to export.
Consider using Templates for repeatable and versioned analysis.
3. Add a Export Statistics task to your Workflow
Once you have the data needed to build your XY plot, click Add new child task and select Export Stats from the task selector.
You can also access the Export Statistics task from within other tasks, such as the Gating task. Have a look below the Logout button.
4. Setup your Export Statistics task
4.1. Select your Files
Select the Files you want to export statistics for and click Next or click Features.
Most dropdowns in OMIQ allow you to filter the list, just start typing. You can even filter by metadata.
4.2. Select your Features
Select the Filters you want to export Feature Measures for → select the Feature Measures you want to export → select the Features you want the selected Feature Measures of → go to the Counts tab.
In this example, we will export the Mean Fluorescent Intensity for FITC on our positive cells.
4.3. Select your Counts
Select the Filters you want to export Count Measures for → select the Count Measures you want to export, then skip to Metadata.
In this example, we will export the Percent of live cells that are FITC+ (pos) cells and the Percent of singlets that are live.
4.4. Select your Metadata
It is very important to add the metadata necessary to build your XY plot. Select the necessary Metadata Dimensions then go to Configuration.
Go back to Step (1) if you don't see the Metadata you need in the Metadata Dimensions.
4.5. Configure your Export settings
Select Prism in the Export File Format dropdown. Adjust any other settings and click Export or Run Export Stats.
4.6. Download your File
Navigate the the Results tab within the Export Statistics task and click the cloud icon to download your file.
5. Open and Analyze your GraphPad Prism File
5.1. Extract and Rearrange your Multiple Variable Table
Open your GraphPad Prism file and click Analyze → select the Extract and Rearrange analysis and click OK. The Format of results table will be set to XY for linear and nonlinear regression by default → navigate to the Data arrangement tab → define your variables and click OK.
In this example we are viewing the percentage of our fluorescent marker (response Y variable) over a serial dilution (independent X variable) of the drugs (Grouping variable) of interest. We have included the repeats (Subject/replicate variable) in the dataset for statistical power.
5.2. Fit a Curve with Non Linear Regression and Perform your EC50 Analysis
Completion of the previous step should automatically navigate you to your reshaped table in the Results section. From here, select Fit a Curve with Non Linear Regression → select the relevant equation for your data and click OK. This will generate a new Results table that will open automatically - shown here with the EC50 values for our 16 drug candidates.
In this example we have chosen to use [Agonist] vs. response (three parameters). The best equation will depend on your data and experimental design.
You will find a outlier detection tool in the Method tab of the Non-linear Regression analysis (not used in this example).
5.3. (Optional) Express your Creative Flair on your Graph
If the default plot is not to your liking, you can use the many handy tools in GraphPad Prism to adjust it. Many of these tools can be accessed by double clicking different aspects of your Graph, or in the Change section of the toolbar shown in the image above.
You can share your result easily using Prism Cloud