Hello everyone, after the last live broadcast: the enrichment analysis results are not ideal: how to find all the terms you want from thousands of terms?
Someone asked on site b, does this count as artificially modifying the results of enrichment analysis?
Up owner: Dr. Shengxin
Enrichment analysis dilemma
When performing enrichment analysis, results containing thousands of terms are often obtained, which makes subsequent research difficult.
my solution
In the live broadcast, I introduced a method to find all the terms you want from thousands of terms. This method is to first use filtering and sorting methods to narrow the search scope, and then use manual screening methods to finally determine the required terms.
Regarding the issue of artificially modifying the enrichment analysis results mentioned in the live broadcast, my answer is: not really.
why do i dare to do this
Enrichment analysis is a statistical method, and its results will be affected by many factors, including data quality, algorithm selection, parameter settings, etc. Therefore, the accuracy of enrichment analysis results cannot be completely guaranteed.
In this case, it is a reasonable approach to use manual screening to determine the required terms. Manual screening can eliminate unreasonable results based on the researcher's experience and knowledge. When screening specific terms, you can screen based on our preliminary experiments. For a more detailed explanation, you can refer to the video.
Is it necessary to use the latest database for enrichment analysis?
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The databases used in enrichment analysis are constructed based on a large amount of experimental data, and these databases are continuously updated as new research results are continuously published. Therefore, more accurate results can be obtained by using the latest version of the database for enrichment analysis.
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However, not all enrichment analyzes require using the latest version of the database. If the purpose of the study is simply to understand the general characteristics of a pathway or function, better results can be obtained using older versions of the database.
Finally, you can think about these questions:
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The database used for enrichment analysis is constantly being updated. Why would you want to use the latest version? But do you know whether the database you are using is the latest version?
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From the results of enrichment analysis, why did you choose the top 10 or even the top 1 pathway for in-depth study? Isn’t top2 right? What about the top20? How do you determine that...
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Is the reliability of your research based on experiments or biometric analysis?
postscript
Experiments are the basis of biological research and can directly verify biological hypotheses. Bioinformatics analysis can discover potential patterns from large amounts of data and provide directions for experimental research. The technique of this article is not difficult, it is more of a way of thinking to help everyone develop their own ideas.
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