How to make a gene expression correlation graph?

Question

[unawaz]

Hi all,

I have two gene lists that I created using edgeR of two different conditions. I want to see the direction of commonly expressed genes and make a graph like this for person's correlation. Would I use R for this sort of analysis, and use person's correlation to compare the logFC for both gene lists?

[S]

Hi Unawaz,

There are many ways of representing that but it all depends on the data you have and the information you would like the reader to get. How many genes are we talking about? What is the range of the expression values (or logFC)? For example, Pearson's correlation will generate a value -1 to 1, I am not sure if it will be very informative to plot these values, unless I did not understand your question well.

Answer 1

[h.mon]

The figure you linked uses log2(fold-changes) for panel B, and I think limma-voom normalized values for panel A. With R base graphics, you can plot this type of plot with plot( values_A, values_B ). The correlation can be measured with cor() and the coefficient can be added with lines().