I have RNA-seq data samples regarding several types of cancer that came from the same source, and RNA-seq of control samples from a different source. For the cancer data and for the control data, I run cell type enrichment analysis separately to get an idea about the cell structure of each sample.
Cell type enrichment analysis for the cancer RNA-seq data is called
cancer1, and for the control it's called
The reason I'm applying batch effect is that I have two sources, and I don't want any variation that is not biological.
I'm having some trouble with batch effect correction, when and how should I apply it.
Should I apply
control1 separatly? or should I combine them and only then run the correction?
Or is it better to run the correction before even running the cell type enrichment analysis? like run it on the RNA-seq data to begin with.
Your help will be much appreciated, thank you.