Differential expression analysis between two different cohorts

Question

[leticia]

Hello , please i have two different datasets: TCGA and another one , i need to do a differential expression of genes between them , is it possible ?

[ATpoint]

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.

[leticia]

Conditions are the same and the cohort is ours , so i want to see the difference in genes between them

[ATpoint]

I would use Gene Set Enrichment Analysis. A direct quantitative comparison of the counts is not possible due to batch effects.

[leticia]

Thanks a lot for your help