How to Handle log2foldchange with Zero FPKM in KEGG Enrichment Analysis?
When performing KEGG enrichment analysis, if the FPKM value in the control or treatment group is 0, the log2foldchange can be handled by the following methods:
Add a Small Constant Value
Before calculating log2foldchange, add a small constant (e.g., 0.1 or 0.01) to all FPKM values. This avoids log2(0) while preserving the relative nature of the data. This method is suitable when many genes have low expression.
Use Estimated Values
Replace a 0 FPKM value with an estimated value, such as the lower detection limit or half the lower detection limit. These estimates are determined based on the experiment’s sensitivity and measurement error. This method is appropriate when low-expression genes or high detection limits are common.
Exclude Zero Values
In some cases, genes with a 0 FPKM value can be excluded from the analysis. This approach is applicable when there are many low-expression genes or when zero-expression genes are not of interest.
Use Alternative Statistical Methods:
Instead of log2foldchange, alternative statistical methods—such as t-tests or non-parametric tests like the Wilcoxon rank-sum test—can be used to compare differences between groups. This method is also suitable when low-expression genes or zero-expression genes are not the focus.
Note: The choice of method should be based on a thorough understanding of the data and the experimental design. Preprocessing the data and selecting the appropriate handling method are essential before performing KEGG enrichment analysis. Additionally, performing statistical significance tests and multiple testing corrections helps ensure the reliability and interpretability of the results.
MtoZ Biolabs, an integrated chromatography and mass spectrometry (MS) services provider.
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