DE lncRNA and mRNA correlation analysis
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19 months ago
seta ★ 1.5k

Dear all,

I have a large list of differentially expressed (DE) coding genes and long non-coding RNAs(lncRNA) obtained from an RNA-seq analysis of human (case, control, 6 samples). I would like to do the correlation analysis between DE coding genes and lncRNA. However, I found several papers used the customer script to do the analysis such as pearson or spearman. I'm basically a biologist, not a programmer; I highly appreciate if you could kindly share with me the relevant scripts?

Thanks

lncRNA correlation analysi mRNA • 552 views
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What do you want to correlate? Please add details.

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Sorry, my mean is getting a correlation coefficient between the DE lncRNAs and mRNAs. As far as I know, Pearson and Spearman correlation coefficient can be calculated. I have a large list of DE mRNA and lncRNA that their expression value (CPM value) didn't follow the normal distribution, I transformed the values to log2(CPM+1), but still have not the normal distribution. So, I should calculate the Spearman correlation coefficient between DE lncRNA and mRNA, yes? but, I'm not sure how to do it, exactly?

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RNA-seq data never follows a normal distribution. In R you can use cor.test function.

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