Correlation plot how to improve?

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annkolman78 • 0

@annkolman78-21980

Last seen 5.2 years 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. log correlation plot raw counts enter 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 • 1.1k views

ADD COMMENT • link 5.2 years ago annkolman78 • 0

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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?

ADD REPLY • link 5.2 years ago mikhael.manurung ▴ 280

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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!

ADD REPLY • link 5.2 years ago annkolman78 • 0

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