Hai,
I want to compare the differential expression of genes between diseased and control, from 4 different regions of the brain i.e I have a total of 8 conditions (a diseased and a control from each region). Now I would like to compare the differential expression both between diseased vs control for individual brain region also between each brain region. I have performed Deseq2 before for comparison of gene expression between 2 conditions but I am not sure if it is the best tool for my present study? if yes, what are the things I should keep in mind before I do the analysis?
2) The sample size for 2 of the brain regions is very high (n=50 each) whereas the other 2 regions have smaller sample size (n=12 each) how can I take this into account while dong the analysis?
Thanks in advance
