Error message: in vargenes_vst

[qicheng-ma]

Dear Symphony Team,

I got an error message when I try to build my own reference.

I appreciate your help!

Option 2: Build from scratch (starting with expression)

set.seed(0)
reference = symphony::buildReference(

• ref_exp_full ,
  

• ref_metadata ,
  

• vars = c('donor') ,          # variables to integrate over
  

• K = 100 ,                    # number of Harmony clusters
  

• verbose = TRUE ,             # verbose output
  

• do_umap = TRUE ,             # can set to FALSE if want to run umap separately later
  

• do_normalize = FALSE , # set to TRUE if input counts are not normalized yet

• do_normalize = TRUE ,       # set to TRUE if input counts are not normalized yet
  

• vargenes_method = 'vst' ,    # method for variable gene selection ('vst' or 'mvp')
  

• vargenes_groups = 'donor' ,  # metadata column specifying groups for variable gene selection
  

• topn = 2000 ,                # number of variable genes to choose per group
  

• d = 20 ,                     # number of PCs
  

• save_uwot_path = './testing_uwot_model_2'
  

• )
  Normalizing
  Finding variable genes using vst method
  Error in hvf.info$variance.expected[not.const] <- 10^fit$fitted :
  NAs are not allowed in subscripted assignments
  Calls: -> vargenes_vst -> %>% -> lapply -> FUN
  In addition: Warning message:
  In log(1 + A@x) : NaNs produced
  Execution halted

[qicheng-ma]

Solved