Differential expression analysis between two different cohorts
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Maybe, some details about what the data are would be helpful. So what are the conditions you look at, and are these similar between both cohorts.
Conditions are the same and the cohort is ours , so i want to see the difference in genes between them
I would use Gene Set Enrichment Analysis. A direct quantitative comparison of the counts is not possible due to batch effects.
Thanks a lot for your help