Hi everyone, I have a question regarding my DEG analysis. I have single nuclei sequencing data of three different regions (region 1, 2, and 3). I would like to compare region 1 with 2 and 3. So, I integrated my samples in two different datasets a. 1+2 and b. 1+3. In each dataset I have cases and controls. I did two sets of DEG in each dataset. For example, in dataset “a” I did as follow; first compare region 1 in case vs control (DEG1), second, comparing region 2 in cases vs controls (DEG2). As I have the first region in dataset “b” as. well, I did the same first comparison for dataset “b” (comparing region 1 in cases vs controls). I expected to see the same sets of DEGs in comparison of the region 1 in both datasets. But it didn’t happen because clustering label are different in two datasets. I have some questions regarding this situation: First, how I can have the same labeling when clustering is different? I mean how I can have same DEGs for the same region in two datasets. Second, considering my analysis design do you think that integrating separately is a good idea or it is better to integrate all three datasets? I really appreciate any input.
