Correlation plot how to improve?
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@annkolman78-21980
Last seen 24 months ago

Hi,

I have 2 RNA sequencing datasets and would like to compare their raw read counts.

Their correlation:

cor(log(data$set1), log(data$set2))
0.8734045
cor(data$set1, data$set2)
0.2376726


I have tried to plot them (raw read count and log transformed). I have attached pictures. The log transformed plot look weird. Did I run it correctly?

plot(log(data$set1), log(data$set2))
plot(data$set1, data$set2)


Can I improve the plot? Thank you for you suggestions! log

plot correlation • 239 views
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What do you want to achieve with the correlation analysis?

And could you explain more about these two data sets? Are they from the same experiment but different batches or perhaps they are entirely different?

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Thank you for you answer. I have 2 data sets with the same samples but the RNA was extracted using two different methods. I want to see how they correlate, compare which extraction method is better.

Thank you!