Need help in class assignment analysis after combing multi-datasets using cross-study normalization?

Question

[BioMed]

Dear all,

Here is my situation. I have several datasets from our in-house samples and from GEO. I used combat for cross-study normalization and combined them into one dataset. My colleagues said that we cannot perform such a class assignment analysis with the combined dataset. I wonder is it true? If not, please suggest me some tools/packages for class assignment analysis.

Thank you very much.