Are there Batch effect among different samples?

Question

[charlie]

I collected different RNA-seq samples from different published papers, and I'm analysing and calculating the correlation among the data. Do I need to remove the batch effect or Is there a batch effect among them? If you know about that, please do not hesitate to contact me. Thanks a lot!

[Carambakaracho]

Dear Charlie, this is one of these questions. How is anybody supposed to know if you don't mention the studies.

Are the studies conducted in different labs, by different people with different protocols? ´

[benformatics]

There is probably a batch effect. If you count up the reads, you should then be able to see a batch effect by visualizing the variance via PCA or MDS.