Hi everyone I am not a computational biologist. Having said that, I work with lot of transcriptomic data. Thanks to tools like iDEP, I was able to do fairly well. I have downloaded publicly available data sets (bulk RNA seq) of different cell lines of a cell type.Control vs LPS for every cell line.They all come from different labs. I understand that I have to adjust for batch effects. I did that using DEBbrowser. I have 3 questions on this front. (1) What criteria best suits this kind of data interms of batch correction. I used TMM and combatseq. Batch was just a number manually added by me. Each dataset got a number.
(2) Do I move onto DEG and GO using the batch corrected values or just the original uncorrected raw count ones.?
(3) Comparing the different cell lines under normal ( control conditions) is also of interest to me. Do I have to do a batch correction again on this matrix of only control samples or the global correction that was done (control and LPS) is sufficient?
I would truly be thankful for any help.
Sincerely, a fellow scientist who is way over in his head :)
