Hi, you should be able to run any method on a simple matrix object like your own data. Please send me a sample code that breaks if you think there is a bug. However, I would suggest you to still wrap your data into an ExpressionSet objects, if you have phenotypic covariates data as well. They just make life easier. ExpressionMix class is defined by CellMix for handling the case where you also have associated proportion and/or cell type-specific data that you want to use or compare results with. They also make life easier in this case. But this is not required. Please let me know if you have other issues or troubles with the package. Thank you. Hope this helps. Bests, Renaud