Export a Graph Pad Prism file directly from OMIQ and create a Grouped Plot to analyze matched samples. The example we give below shows how to quickly go from analysis in OMIQ to a paired non-parametric test (Friedman Test with Dunn's post-test) results in GraphPad Prism.
1. Add Metadata to your Dataset
Add any metadata that is needed to build your Grouped plot that will be used to analyze matched samples. At the minimum, you will need to add a column that specifies which samples match (in this case, the Pairing column) and a grouping variable (in this case, the Treatment column)
You can find out how to add metadata to your datasets here.
2. Build your Workflow
Shown above is just an example. Build your workflow in whatever way makes sense for the data you wish to export.
In this example analysis, we have done a clean-up gate and have subsampled to live cells. We have then performed clustering, using FlowSOM and have created a gating task to identify the metaclusters. We then added a Figure task to identify clusters of interest. We are now going to take the counts of our clusters of interest and analyze these as matched samples in GraphPad Prism.
3. Add a Export Statistics task to your Workflow
Once you have the data needed to build your Grouped 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 are only interested in Counts data so have skipped this step.
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 Count for Cluster01 and Cluster07.
4.4. Select your Metadata
It is very important to add the metadata necessary to build your Grouped 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. Change the Format of results table to Grouped for two-way ANOVA → navigate to the Data arrangement tab → define your variables and click OK.
In the example shown, we are viewing the Cluster01|count (Response variable), between our Treatment groups (Column factor variable). We have also specified the way our samples our matched using the Pairing metadata (Row factor variable).
5.2. Perform a Friedman Test with Dunn's Post-Test
Completion of the previous step should automatically navigate you to your reshaped table in the Results section. Note that our data is now arranged such that the matched samples are in the same row. Click on Analyze then navigate to Column analyses. Select One-way ANOVA (and nonparametric or mixed) → select the relevant parameters then click OK. This will generate a new Results table that will open automatically - shown here with the Friedman Test with Dunn's Post-Test for multiple comparisons.
We have then repeated Steps (5.2 and 5.3) for the other response variables of interest (Cluster07|count).
In this example we have chosen to perform the non-parametric test for matched samples, added a multiple comparison with Dunn's post-test correction. The best parameters will depend on your data and experimental design.
5.3. (Optional) Express your Creative Flair on your Graphs
If the default plot is not to your liking, you can use the many handy tools in GraphPad Prism to adjust it.
In this example, we have adjusted the aesthetics of our graphs and created a Box and Whiskers plot. We have adjusted the colors to a color-blind safe palette. We can see that the counts for Cluster 01 was statistically significantly higher in Drug A treatment compared to Media. Cluster07 counts were statistically significantly lower in Drug A and Drug B treatment compared to Media.
You can share your result easily using Prism Cloud