New Count Generation running for too long

[rashikajakhmola]

Hey Team! Thanks for the package.

I am using it to simulate single cell data. Everything works fast enough (within a minute) before I reach the step to generate new counts.

• my sce object is 100 x 2552
• mu_formula = "0+donor_ID + organ_unified + response_treatment_status"

newcount_null_donor_p1 <- simu_new( sce = sce, mean_mat = para_null_donor_p1$mean_mat, sigma_mat = para_null_donor_p1$sigma_mat, zero_mat = para_null_donor_p1$zero_mat, quantile_mat = NULL, copula_list = donorid_copula$copula_list, n_cores = 2, family_use = "nb", input_data = donorid_data$dat, new_covariate = donorid_data$newCovariate, important_feature = donorid_copula$important_feature, filtered_gene = donorid_data$filtered_gene )

This has been running for > 24 hours now. Should it take this long for 100 genes?

[SONGDONGYUAN1994]

Dear Rashika,

That sounds extremely weird. Usually 100 genes only take a few mins. Did you mean that you have finished all previous steps and got stuck at simu_new? If yes, you may check if mean_mat or sigma_mat have any abnormal values; e.g., a mean expression value is over 10,000 and it looks like a outlier.

[rashikajakhmola]

Thanks, Dongyuan! I did have outliers. Worked pretty quickly post filtering them. Appreciate your help :)