Question: Correlation plot how to improve?
gravatar for annkolman78
29 days ago by
annkolman780 wrote:


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

Their correlation:

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

I have tried to plot them (raw read count and log transformed). I have attached pictures.log correlation plot raw countsenter image description here 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 • 64 views
ADD COMMENTlink modified 29 days ago • written 29 days ago by annkolman780

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?

ADD REPLYlink written 29 days ago by mikhael.manurung200

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!

ADD REPLYlink modified 29 days ago • written 29 days ago by annkolman780
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