x or y has vectors with zero standard deviation; consider setting use_nan = TRUE

[Pinolinoo]

Why do I get this error message when running generate_gold_standart?

[rcannood]

Can you provide me with a small reproducible example? Which version of dyngen is this ?

[Pinolinoo]

Thank you very much for replying!
It's version 1.0.3

I ran this script:

`set.seed(1)

backbone <- backbone_bifurcating()
config <-
initialise_model(
backbone = backbone,
num_tfs = nrow(backbone$module_info),
num_targets = 500,
num_hks = 500,
verbose = FALSE
)

model <- generate_tf_network(config)
plot_feature_network(model, show_targets = FALSE)
model <- generate_feature_network(model)
plot_feature_network(model)
model <- generate_kinetics(model)
model <- generate_gold_standard(model)

model <- generate_cells(model)
plot_simulations(model)

write_rds(model, "mode_circle.rds", compress = "gz")
`

[rcannood]

Can you update to 1.0.4 ? It was caused by an update to an underlying package.

[Pinolinoo]

Ok so I updated to 1.0.4 and now when I run the same script it gives me the error:

Error in x$.self$finalize() : attempt to apply non-function Error in x$.self$finalize() : attempt to apply non-function Error in x$.self$finalize() : attempt to apply non-function Error in (function (x) : attempt to apply non-function

After running generate_gold_standart()

However if I run the function again afterwards it doesn't give me an error!

[Pinolinoo]

Also when continuing then and wanting to export the data I get the following errors:

when trying with seurat as in:

library(Seurat) seurat <- as_seurat(model) write_rds(seurat, "dataset_seurat.rds")

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

also with anndata:
library(anndata) ad <- as_anndata(model) ad$write_h5ad("dataset.h5ad")

I get

ad <- as_anndata(model) Error in as(log2(counts + 1), "dgCMatrix") : no method or default for coercing "numeric" to "dgCMatrix"

I suppose there is still something going wrong during the simulation!