Error in UseMethod("family"): no applicable method for 'family' applied to an object of class "NULL"

[MohammadIzadi]

Hi,
Thanks for developing scDesign3. I have SingleCellExperiment object. I want to simiulate it with scDesign3. but i get this error.

example_simu <- scdesign3(

• sce = data,
  

• assay_use = "counts",
  

• celltype = "celltype",
  

• pseudotime = NULL,
  

• spatial = NULL,
  

• other_covariates = NULL,
  

• mu_formula = "celltype",
  

• sigma_formula = "celltype",
  

• family_use = "gaussian",
  

• n_cores = 1,
  

• corr_formula = "celltype",
  

• )

Input Data Construction Start
Input Data Construction End
Start Marginal Fitting
Marginal Fitting End
Start Copula Fitting
Convert Residuals to Multivariate Gaussian
Error: BiocParallel errors
1 remote errors, element index: 1
5 unevaluated and other errors
first remote error:
Error in UseMethod("family"): no applicable method for 'family' applied to an object of class "NULL".

Can you help me to fix it please?

[SONGDONGYUAN1994]

Hi,

Could you check the format of your input data? I saw you used assay_use = 'counts' (count data rather than log transformed data), which usually means family_use should be nb or poisson rather than gaussian.