Result data frame is NULL

[StefTesta]

Hi Simone,

Thank you for this great tool.

I followed your vignette and tried to run a simple analysis comparing tumor versus normal cells from 3 samples.

Everything when smoothly up to this point:

set.seed(61217)
res <-  distinct_test(x = sce_lms_endo, 
                    name_assays_expression = "logcounts",
                    name_cluster = "classification_2",
                    name_sample = "sample",
                    design = design,
                    column_to_test = 2,
                    min_non_zero_cells = 20,
                    n_cores = 4)

2 groups of samples provided
Covariates detected
Data loaded, starting differential testing
Differential testing completed, returning results

Then then when I tried to calculate the log2FC I then got this error:

res = log2_FC(res = res,
               x = sce_lms_endo, 
               name_assays_expression = "cpm",
               name_group = "classification",
               name_cluster = "classification_2")

Error in log2_FC(res = res, x = sce_lms_endo, name_assays_expression = "cpm",  : 
  is.data.frame(res) is not TRUE

It seems like the "res" data.frame was not created when running distinct_test.

Could you provide some insight in why this might be happening?

Thank you,
Stefano

[SimoneTiberi]

Hi @StefTesta,
I am glad you appreciate our tool.

Did you modify res after running distinct_test?
res is not a data.frame, so either it was modified after distinct_test or there was an error in distinct_test, and res is empty.

Can you do 2 things:

• check class(res) and head(res);
• write the full script you run with messages.

Thanks