best way to correlate RNA-Seq data?

[PFS]

I would like to find out if there is correlation between two tables consisting of RNA abundance estimates (rows = genes, columns = samples).

For example, suppose I have two experiments E1 and E2 with same conditions/samples (S1, S2, S3, S4). I would like to know if the trend observed for a given gene in E1 across S1-S2-S3-S4 is the same as the trend observed for the same gene in E2.

My stats background is really poor, but I basically think I need to find if how two matrices correlate with each other. I read something about the Mantel test, but I don't have distances, I have expression/abundance estimates.

Also, what if the two tables are from different data source (e.g. microarray and RNA-Seq)?

Thanks!