Export a Graph Pad Prism file directly from OMIQ and create a Column plot. The example we give below shows how to quickly go from analysis in OMIQ to t-test results in GraphPad Prism.
1. Add Metadata to your Dataset
Add any metadata that is needed to build your Column plot. For this example, the Grouping variable (X-axis) is Condition (HD: healthy donor, CLL: chronic lymphocytic leukemia).
You can find out how to add metadata to your datasets here.
2. Build your Workflow
Shown above is just an example (note that the fcs files were already compensated). Build your workflow in whatever way makes sense for the data you wish to export.
In this example analysis, we have samples taken in several separate batches and have therefore combined the samples using CyCombine. We have then performed manual phenotyping, reviewed this in the figure task and will now export the phenotypes to compare HD and CLL samples for statistical significance.
3. Add a Export Statistics task to your Workflow
Once you have the data needed to build your Column 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 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 Percent of Total cells that are CD19+CD20+ (B cells), CD4+ or CD8+.
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 Column for t-tests, one-way ANOVA, etc → navigate to the Data arrangement tab → define your variables and click OK.
In the example shown, we are viewing the percentage of our total cells that are CD19+CD20+ B cells (Response variable), between our Conditions (Grouping variable). We have then repeated this step for the other response variables of interest (CD8+|percent total and CD4+|percent total).
5.2. Perform a t-test
Completion of the previous step should automatically navigate you to your reshaped table in the Results section. From here, select Compare two groups: t test, Mann-Whitney test, Wilcoxon test → select the relevant parameters then click OK. This will generate a new Results table that will open automatically - shown here with the Unpaired t test results for CD19+CD20+ (B cells)|percent_total.
We have then repeated this step for the other response variables of interest (CD8+|percent total and CD4+|percent total).
In this example we have chosen to use the default settings for Unpaired t Test. The best equation 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 Column Plots and made a layout. We can see that there were significantly more CD19+CD20+ B cells in CLL samples compared to HD samples. There was no significant difference in CD4+ or CD8+ T cells.
You can share your result easily using Prism Cloud