Combining data - best practice

[Theresa Suckert]

Hello,

I have measurements from ~20 brains (~8 GB) from one experimental cohort. The aim is to evaluate them all together, but I'm not sure what the best practice is. Intuitively, I would load them all into one R project and perform the preprocessing steps on the complete data set to ensure that all samples are preprocessed in the same way. However, this probably will exceed the RAM on my workstation (256 GB) and I`m not very keen on testing that. I've seen some people are doing the preprocessing on each sample individually and then combining them together. But from the first look of my data, it appears that I have some batch-to-batch variation between the samples.

What would be considered the best practice approach here? I don't want to inadvertently bias my data by messing up the preprocessing.

Thank you very much!

- Theresa