no logcount value shows on object after preprocess_cds

[shangguandong1996]

Hi, I am new to monocle3. But I find it is hard for me to find the logcount result on object even after running preprocess_cds. But accroding to help document, it seems that it will do log-norm during preprocess_cds.

library(monocle3)

expression_matrix <- readRDS(url("https://depts.washington.edu:/trapnell-lab/software/monocle3/celegans/data/packer_embryo_expression.rds"))

cds <- new_cell_data_set(expression_data = expression_matrix)
cds <- preprocess_cds(cds, num_dim = 50)

> cds
class: cell_data_set 
dim: 20222 6188 
metadata(1): cds_version
assays(1): counts
rownames(20222): WBGene00010957 WBGene00010958 ... WBGene00021594
  WBGene00007064
rowData names(0):
colnames(6188): AAACCTGCAAGACGTG-300.1.1 AAACCTGGTGTGAATA-300.1.1 ...
  TGCGGGTAGTACTTGC-b02 TTTGTCAAGTACACCT-b02
colData names(2): cell Size_Factor
reducedDimNames(1): PCA
mainExpName: NULL
altExpNames(0):

> sessionInfo()
R version 4.2.0 (2022-04-22)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS Stream 8

Matrix products: default
BLAS:   /opt/sysoft/R-4.2.0/lib64/R/lib/libRblas.so
LAPACK: /opt/sysoft/R-4.2.0/lib64/R/lib/libRlapack.so

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C               LC_TIME=en_US.UTF-8       
 [4] LC_COLLATE=en_US.UTF-8     LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                  LC_ADDRESS=C              
[10] LC_TELEPHONE=C             LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] stats4    stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] monocle3_1.2.9              SingleCellExperiment_1.18.0 SummarizedExperiment_1.26.1
 [4] GenomicRanges_1.48.0        GenomeInfoDb_1.32.2         IRanges_2.30.0             
 [7] S4Vectors_0.34.0            MatrixGenerics_1.8.0        matrixStats_0.62.0         
[10] Biobase_2.56.0              BiocGenerics_0.42.0        

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.8.3              lattice_0.20-45           listenv_0.8.0            
 [4] assertthat_0.2.1          digest_0.6.29             utf8_1.2.2               
 [7] parallelly_1.31.1         R6_2.5.1                  plyr_1.8.7               
[10] ggplot2_3.3.6             pillar_1.7.0              sparseMatrixStats_1.8.0  
[13] zlibbioc_1.42.0           rlang_1.0.3               rstudioapi_0.13          
[16] minqa_1.2.4               irlba_2.3.5               nloptr_2.0.3             
[19] Matrix_1.4-1              splines_4.2.0             lme4_1.1-30              
[22] igraph_1.3.1              RCurl_1.98-1.6            munsell_0.5.0            
[25] DelayedArray_0.22.0       compiler_4.2.0            pkgconfig_2.0.3          
[28] globals_0.15.0            tidyselect_1.1.2          tibble_3.1.7             
[31] GenomeInfoDbData_1.2.8    codetools_0.2-18          fansi_1.0.3              
[34] future_1.25.0             crayon_1.5.1              dplyr_1.0.9              
[37] MASS_7.3-57               bitops_1.0-7              grid_4.2.0               
[40] nlme_3.1-157              gtable_0.3.0              lifecycle_1.0.1          
[43] DBI_1.1.2                 magrittr_2.0.3            scales_1.2.0             
[46] cli_3.3.0                 XVector_0.36.0            DelayedMatrixStats_1.18.0
[49] ellipsis_0.3.2            generics_0.1.2            vctrs_0.4.1              
[52] boot_1.3-28               tools_4.2.0               glue_1.6.2               
[55] purrr_0.3.4               parallel_4.2.0            colorspace_2.0-3         
[58] terra_1.6-7 

Best wishes

Guandong Shang