T1_Method2 tutorial doesn't seem to match the actual file

[dd315]

The tutorial says there are two environments, but in fact the sample data has only one environment. I don't know if it's my misunderstanding.

[datasome]

Dear dd315,

Many thanks for pointing this out - much appreciated - I've just fixed it in all three tutorials, e.g. in https://github.com/ventolab/CellphoneDB/blob/master/notebooks/T1_Method1.ipynb.

Best,

Robert.

[dd315]

Dear dd315,

Many thanks for pointing this out - much appreciated - I've just fixed it in all three tutorials, e.g. in https://github.com/ventolab/CellphoneDB/blob/master/notebooks/T1_Method1.ipynb.

Best,

Robert.

Thank you so much for your reply. In fact, what confused me more is how to use CellphoneDB when there are two groups, such as two different microenvironments, tumor samples and normal samples, treatment group and control group, and so on. Is it directly defining two groups in Microenvironments file, or manually comparing after running cpdb_statistical_analysis_method repeatedly?

[datasome]

Hi dd315,

My apologies for not replying earlier - I was away for a few days. Yes, no interactions will be considered during CellphoneDB analysis between cell type A and cell type B if those two cell types are assigned to different microenvironments in the microenvironments file. Does that make sense?

Best,

Robert.