You can use PCA. Here are the links for how to use it :

https://tavareshugo.github.io/data-carpentry-rnaseq/03_rnaseq_pca.html

This article discussed the PCA for RNA-Seq data in details :

https://academic.oup.com/nar/article/43/16/7664/1076142#33539083

If you want to understand how PCA works for RNA-Seq data:

https://www.biostars.org/p/280615/

https://www.youtube.com/watch?v=FgakZw6K1QQ&feature=youtu.be

https://www.youtube.com/watch?v=oRvgq966yZg&feature=youtu.be

Differntial expression is a good point to decipher groups, but as Asgar Hussain said, PCA will give you a good view on differences in groups.

fred

You can also do a correlation test (e.g. Pearson, Spearman) between two replicates of a condition to check how similar, or dissimilar they are. You can do in R using

cor.test ( rep1_cond1,rep2_cond1,met,method = "pearson")

where rep1_cond1,rep2_cond1 are two replicates for condition 1.