How to show that correlation from one method is more significant than other method?

Question

[rheab1230]

Hello All,

I am working on a project wherein we are comparing two methods.

In one method: we see that majority of genes are showing improvement in correlation between predicted and residual expression in comparison to other method.

For example: let says we have 500 genes and are using elastic net and Bayesian method to model gene expression.

method1: 378/500 shows improvement in correlation whereas method2: 122/500: gives good correlation score.

How can we say significantly that method 1 is better in comparison to method2?

Basically, how can I say that 378 genes out of 500 genes their improvement is significant in comparison to method 2?

Is there any way to elucidate this information?

[Shred]

It's not clear what these methods are doing. Maybe use the mean squared error over all the genes?

[rheab1230]

Basically both the method produce a gene expression model, we then use the model to predict expression on the remaining datasets and generate a correlation between predicted and actual expression.

[Shred]

Then the MSE would be enough.