Rphenograph clustering codes not working

[zoqaiyum]

Hi @nilseling

I created an "sce" object for my images and masks and now I am following this protocol (https://bodenmillergroup.github.io/IMCDataAnalysis/cell-phenotyping.html#clustering) to perform clustering using Rphenograph (section 9.2.1).

Using your code, I simply replaced "spe" to "sce" since my object is a single class experiment object but I am getting the following error:

It appears that there is no "exprs" in my sce object. How should I proceed?

Many thanks.

[nilseling]

Please read through one of the earlier sections on data transformation: https://bodenmillergroup.github.io/IMCDataAnalysis/read-data.html