I have some cases with duplicate identifiers (i.e., identifiers that map to the same molecule) that meet the cutoff.
I want to do a core analysis in IPA and look at protein-protein interactions. Which method is the most applicable in this case?
Resolve duplicates using median?
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Mathilde Resell For dealing with duplicates in Ingenuity Pathway Analysis (IPA), you can choose the greatest or lowest expression value, take the mean or median expression value, or utilize a custom rule.
If you wish to employ the median technique, you may do it in IPA by following these steps:
In IPA, open the dataset with the duplicate identifiers.
At the upper right corner of the table, click the "Resolve Duplicates" button.
Choose the "Median" option under "Resolve duplicate identifiers by" in the pop-up box.
Choose the columns containing the expression data that you wish to utilize for the analysis.
To apply the modifications to the dataset, click the "Resolve Duplicates" button.
Once the duplicates have been addressed, you may use IPA to do a core analysis to investigate protein-protein interactions. The core analysis will produce a list of enriched pathways, biological functions, and upstream regulators linked to the input data.
To do a core analysis in IPA, follow these steps:
On the IPA main menu, select the "Core Analysis" tab.
As input data, use the resolved dataset.
Choose the right species and analysis parameters.
To begin the analysis, click the "Run Analysis" button.
When the analysis is finished, you may look at the results on the "Results" tab. The "Networks" view visualizes protein-protein connections, while the "Pathways" and "Functions" views investigate enriched pathways and biological functions.
Mathilde Resell
Yes, resolving duplicates using median is the most applicable method in this case. This method will ensure that the duplicates are combined into a single data point that represents the average value of the duplicates, which can then be used in the downstream analysis. This will also prevent any biases or noise caused by the duplicates from affecting the core analysis results.
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