Hi!
I have 8 scrnaseq samples, consisting of 4 genotypes and 2 phenotypes (geno1 - control, treatment / geno2 - control, treatment / geno3 - control, treatment / geno4 - control, treatment).
First, I want to check the treatment effect for each genotype, i.e. (geno1 control vs. geno1 treatment), (geno2 control vs. geno2 treatment), …
Then, I would like to perform pairwise comparisons between different genotypes under the same treatment conditions., namely, (geno1 treatment vs. geno2 treatment), (geno1 treatment vs. geno3 treatment) and (geno1 treatment vs. geno4 treatment).
In this experimental design, should I integrate the all 8 samples and then perform pairwise comparisons, or should I integrate each of the two samples separately and then perform the comparisons? Which approach is right for me?
Thanks!
