Error while running variancePartition::dream()
Entering edit mode
Junghoon ▴ 10
Last seen 14 days ago
South Korea

I need help with a weird error I'm getting from variancePartition::dream().

I want to get a list of genes with sex-biased expression from my RNA-Seq data. The count matrix (count_data) consists of 27,584 samples (columns) and 34,155 genes (rows). The samples are from 10,824 individuals (case_id), hence ~2.6 samples from each individual on average. I'm trying to model three fixed effects (sex, tissue_cancer, batch) and one random effect (case_id) using the dream pipeline as illustrated here. Here is the error-producing part of my code:

dgelist = DGEList(counts = count_data,
                  samples = sample_metadata,
                  group = sample_metadata$sex,
                  genes = gene_metadata)

k = filterByExpr(dgelist)

dgelist = dgelist[k, , keep.lib.sizes = F]

dgelist = calcNormFactors(dgelist, method = "TMM")

form = ~ sex + tissue_cancer + batch + (1|case_id)

v = voomWithDreamWeights(dgelist, form, sample_metadata, BPPARAM = MulticoreParam(12))
# Memory usage to store result: >69.7 Gb                                
# Dividing work into 100 chunks...                                      
# Total:4329 s                                                

dfit = dream(v, form, sample_metadata, computeResiduals = F, BPPARAM = MulticoreParam(4))
# Dividing work into 100 chunks...            
# Error in env[[as.character(i)]] <- value :                     
#   wrong args for environment subassignment                     
# Calls: dream ... bploop -> bploop.iterate -> <Anonymous> -> add_inorder                                                                                                                                            
# In addition: Warning message:                                       
# In seq.default(a = val) : partial argument match of 'a' to 'along.with'
# Execution halted                                                  
# Error: unexpected '=' in "="                                
# Execution halted

I really have no idea what the error means and what I should do to make it work. Any advice would be very much appreciated!

Session Info

> sessionInfo()
R version 4.0.4 (2021-02-15)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 18.04.5 LTS

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/blas/
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/

 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C               LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8     LC_MONETARY=en_US.UTF-8   
 [6] LC_MESSAGES=en_US.UTF-8    LC_PAPER=en_US.UTF-8       LC_NAME=C                  LC_ADDRESS=C               LC_TELEPHONE=C            

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

other attached packages:
 [1] RColorBrewer_1.1-2          variancePartition_1.20.0    BiocParallel_1.24.1         forcats_0.5.1               stringr_1.4.0              
 [6] dplyr_1.0.5                 purrr_0.3.4                 readr_1.4.0                 tidyr_1.1.3                 tibble_3.1.1               
[11] tidyverse_1.3.1             scales_1.1.1                rstudioapi_0.13             magrittr_2.0.1              ggpubr_0.4.0               
[16] ggplot2_3.3.3               fst_0.9.4                   edgeR_3.32.1                limma_3.46.0                e1071_1.7-6                
[21] dtplyr_1.1.0                DESeq2_1.30.1               SummarizedExperiment_1.20.0 Biobase_2.50.0              MatrixGenerics_1.2.1       
[26] matrixStats_0.58.0          GenomicRanges_1.42.0        GenomeInfoDb_1.26.7         IRanges_2.24.1              S4Vectors_0.28.1           
[31] BiocGenerics_0.36.1         data.table_1.14.0           cowplot_1.1.1              

loaded via a namespace (and not attached):
 [1] minqa_1.2.4            colorspace_2.0-0       ggsignif_0.6.1         ellipsis_0.3.1         class_7.3-18           rio_0.5.26            
 [7] colorRamps_2.3         XVector_0.30.0         fs_1.5.0               proxy_0.4-25           bit64_4.0.5            AnnotationDbi_1.52.0  
[13] fansi_0.4.2            lubridate_1.7.10       xml2_1.3.2             codetools_0.2-18       splines_4.0.4          doParallel_1.0.16     
[19] cachem_1.0.4           geneplotter_1.68.0     knitr_1.33             jsonlite_1.7.2         nloptr_1.2.2.2         pbkrtest_0.5.1        
[25] broom_0.7.6            annotate_1.68.0        dbplyr_2.1.1           compiler_4.0.4         httr_1.4.2             backports_1.2.1       
[31] assertthat_0.2.1       Matrix_1.3-2           fastmap_1.1.0          cli_2.4.0              prettyunits_1.1.1      tools_4.0.4           
[37] gtable_0.3.0           glue_1.4.2             GenomeInfoDbData_1.2.4 reshape2_1.4.4         Rcpp_1.0.6             carData_3.0-4         
[43] cellranger_1.1.0       vctrs_0.3.7            nlme_3.1-152           iterators_1.0.13       xfun_0.22              lme4_1.1-26           
[49] openxlsx_4.2.3         rvest_1.0.0            lifecycle_1.0.0        gtools_3.8.2           statmod_1.4.35         rstatix_0.7.0         
[55] XML_3.99-0.6           MASS_7.3-53.1          zlibbioc_1.36.0        hms_1.0.0              curl_4.3               memoise_2.0.0         
[61] stringi_1.5.3          RSQLite_2.2.7          genefilter_1.72.1      foreach_1.5.1          caTools_1.18.2         boot_1.3-27           
[67] zip_2.1.1              rlang_0.4.10           pkgconfig_2.0.3        bitops_1.0-7           lattice_0.20-41        bit_4.0.4             
[73] tidyselect_1.1.0       plyr_1.8.6             R6_2.5.0               gplots_3.1.1           generics_0.1.0         DelayedArray_0.16.3   
[79] DBI_1.1.1              pillar_1.6.0           haven_2.4.1            foreign_0.8-81         withr_2.4.2            survival_3.2-10       
[85] abind_1.4-5            RCurl_1.98-1.3         modelr_0.1.8           crayon_1.4.1           car_3.0-10             KernSmooth_2.23-18    
[91] utf8_1.2.1             progress_1.2.2         locfit_1.5-9.4         grid_4.0.4             readxl_1.3.1           blob_1.2.1            
[97] reprex_2.0.0           xtable_1.8-4           munsell_0.5.0
variancePartition limma BiocParallel • 98 views
Entering edit mode
Junghoon ▴ 10
Last seen 14 days ago
South Korea

I did a few tests. I still have no idea what the error messages really mean, but now I'm pretty sure that this is a memory issue because the error always occurs immediately once the memory usage reaches the limit. I found an inelegant but working solution.


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