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