`MOFAobject@expectations` is empty list

Question

[Dan]

Hello

I run the tutorial (https://raw.githack.com/bioFAM/MOFA2_tutorials/master/R_tutorials/CLL.html)

library(MOFA2)
library(MOFAdata)
library(data.table)
library(ggplot2)
library(tidyverse)

utils::data("CLL_data") 
MOFAobject <- create_mofa(CLL_data)

MOFAobject

data_opts <- get_default_data_options(MOFAobject)
model_opts <- get_default_model_options(MOFAobject)
model_opts$num_factors <- 15

train_opts <- get_default_training_options(MOFAobject)
train_opts$convergence_mode <- "slow"
train_opts$seed <- 42

MOFAobject <- prepare_mofa(MOFAobject,
                           data_options = data_opts,
                           model_options = model_opts,
                           training_options = train_opts
)

MOFAobject@expectations

only get

list()

sessionInfo()

R version 4.2.3 (2023-03-15 ucrt)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 22621)

Matrix products: default

locale:
[1] LC_COLLATE=English_United States.utf8  LC_CTYPE=English_United States.utf8    LC_MONETARY=English_United States.utf8
[4] LC_NUMERIC=C                           LC_TIME=English_United States.utf8

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

other attached packages:
 [1] forcats_0.5.1     stringr_1.5.0     dplyr_1.1.0       purrr_1.0.1       readr_2.1.2       tidyr_1.3.0
 [7] tibble_3.2.1      tidyverse_1.3.1   ggplot2_3.4.2     data.table_1.14.6 MOFAdata_1.12.0   MOFA2_1.6.0

loaded via a namespace (and not attached):
 [1] matrixStats_0.63.0   fs_1.5.2             lubridate_1.9.2      filelock_1.0.2       RColorBrewer_1.1-3
 [6] httr_1.4.4           tools_4.2.3          backports_1.4.1      utf8_1.2.3           R6_2.5.1
[11] HDF5Array_1.20.0     uwot_0.1.14          DBI_1.1.2            BiocGenerics_0.42.0  colorspace_2.1-0
[16] rhdf5filters_1.4.0   withr_2.5.0          tidyselect_1.2.0     compiler_4.2.3       cli_3.5.0
[21] rvest_1.0.2          basilisk.utils_1.8.0 xml2_1.3.3           DelayedArray_0.18.0  scales_1.2.1
[26] digest_0.6.31        rmarkdown_2.19       basilisk_1.8.1       pkgconfig_2.0.3      htmltools_0.5.4
[31] MatrixGenerics_1.4.3 dbplyr_2.1.1         fastmap_1.1.0        rlang_1.1.1          readxl_1.3.1
[36] rstudioapi_0.13      farver_2.1.1         generics_0.1.3       jsonlite_1.8.4       magrittr_2.0.3
[41] Matrix_1.5-3         Rcpp_1.0.10          munsell_0.5.0        S4Vectors_0.34.0     Rhdf5lib_1.14.2
[46] fansi_1.0.4          reticulate_1.26      lifecycle_1.0.3      stringi_1.7.12       yaml_2.3.6
[51] rhdf5_2.36.0         Rtsne_0.16           plyr_1.8.8           grid_4.2.3           parallel_4.2.3
[56] ggrepel_0.9.3        crayon_1.5.2         dir.expiry_1.4.0     lattice_0.20-45      haven_2.4.3
[61] cowplot_1.1.1        hms_1.1.1            knitr_1.41           pillar_1.9.0         reshape2_1.4.4
[66] stats4_4.2.3         reprex_2.0.1         glue_1.6.2           evaluate_0.19        modelr_0.1.8
[71] png_0.1-8            vctrs_0.5.2          tzdb_0.2.0           cellranger_1.1.0     gtable_0.3.3
[76] assertthat_0.2.1     xfun_0.36            broom_0.7.12         pheatmap_1.0.12      IRanges_2.30.1
[81] corrplot_0.92        timechange_0.2.0     ellipsis_0.3.2

Can you please let me know what is wrong with my codes?

Thanks

[GenoMax]

For awareness, this is cross-posted at Bioconductor site : https://support.bioconductor.org/p/9151950/

If you get an answer on either site please post it on other so the thread does not stay open.

[Dan]

Sure. Thanks