diffCyt and edgeR return different results

[LazDaria]

Hi, thank you for this helpful package. I raised an issue in the cytofWorkflow Github repo, because I am getting different results with diffcyt and edgeR. While I get reasonable results with edgeR, diffcyt returns NA p-values and zero abundance for some clusters across all samples (which is not true).

For now, I will just use edgeR directly. However, if you have time to look into this issue, it would be nice to know where the difference is coming from or whether the way I input my data to diffcyt is wrong.

Thank you!