Correlation analysis for low expressed genes
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Entering edit mode
17 months ago
kmsh410 ▴ 40

Dear all, I am doing a correlation analysis on few targeted genes and I found there some genes that are low expressed. For example, a gene expression data for two gene with 100 subjects below:

        Gene A   Gene B 
Subject1  0       45
Subject2  0       42
Subject3  0       55
Subject4  0.1     78
Subject5  0.03    66
   ...
Subject98 0.09    69
Subject99 0       47
Subject100 0      44

However, there are many zero values in Gene A, and only three subjects are detected little gene expression on Gene A. Here is my question. Is it reasonable to use Spearman correlation to capture the relationship between Gene A and Gene B? I would greatly appreciate it if you kindly give me some feedback.

correlation analysis • 272 views
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Entering edit mode
17 months ago

One option is to use the samples with only non-zero expression values. Other option is to perform permutations and calculate a p-value.

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Appreciate your suggestions. I will take a look some permutation approaches and other tools that could analyze the zero-inflated data.

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