some parameters are set to the CSIDE vignette values, which are intended for testing but not proper execution.

[sopenaml]

Hi,

Thank you very much for developing these great packages. Could you elaborate why the following warning? Warning message: In run.CSIDE.general(myRCTD, X1, X2, barcodes, cell_types, cell_type_threshold = cell_type_threshold, : run.CSIDE.general: some parameters are set to the CSIDE vignette values, which are intended for testing but not proper execution. For more accurate results, consider using the default parameters to this function.

I have a visium data set, where the cell type of interest seems to have very low weights per spot (around between 5-10%) and in few spots. So in order to run.CSIDE.single I have to do:

run.CSIDE.single(rctd.a4, 
                            explanatory.variable, 
                            doublet_mode = FALSE, 
                             cell_types =  c("cell_type2","cell_type1")") , 
                            fdr = 0.05,
                            weight_threshold = 0.07, 
                            cell_type_threshold = 28) 

As you can see, the thresholds required for the analysis are way below the defaults. And I was wondering if this is OK to use of what would you advice? Thank you very much for your time and assistance.