Error when running simulateDE

[Benjamin-Hing]

Hi,

I am trying to perform power calculation using the powsimR. I ran the analysis as specified in the vignette but I keep encountering an error after running the simulateDE function:

#Estimation
estparam_gene <- estimateParam(countData = as.data.frame(GetAssayData (astrocyte_SCT_counts, assay = "SCT", slot = "count")),
                          readData = NULL,
                          batchData = NULL,
                          spikeData = NULL,
                          spikeInfo = NULL,
                          Lengths = NULL, MeanFragLengths = NULL,
                          RNAseq = 'singlecell', Protocol = 'UMI',
                          Distribution = 'ZINB', Normalisation = "sctransform",
                          GeneFilter = 0.05, SampleFilter = 5,
                          sigma = 1.96, NCores = NULL, verbose = TRUE)

# define log fold change
p.lfc <- function(x) sample(c(-1,1), size=x,replace=T)*rgamma(x, shape = 1, rate = 2)
# set up simulations
setupres <- Setup(ngenes = 10000, nsims = 25,
                  p.DE = 0.05, pLFC = p.lfc,
                  n1 = c(50, 100, 200, 400, 800), n2 = c(50, 100, 200, 400, 800),
                  Thinning = NULL, LibSize = 'equal',
                  estParamRes = estparam_gene,
                  estSpikeRes = NULL,
                  DropGenes = TRUE,
                  setup.seed = 5299, verbose = TRUE)

#Simulation
simres <- simulateDE(SetupRes = setupres,
                     Prefilter = "FreqFilter", Imputation = NULL,
                     Normalisation = 'sctransform', Label = 'none',
                     DEmethod = "DESeq2-ZINB-WaVE", DEFilter = FALSE,
                     NCores = NULL, verbose = TRUE)

I encounter this error after running the simulateDE function:

Error in DESeq2::DESeqDataSetFromMatrix(countData, coldat, ~design, tidy = FALSE, :
ncol(countData) == nrow(colData) is not TRUE

Could I please get some help and advice about how to address this problem?

(1) Although I have input the countData when I ran the estimateParam function at the start, I am unsure where to input the colData so that ncol(countData) == nrow(colData) would be TRUE. Or is there something I have not done correctly in the workflow?

(2) On a related note, is there way to include a model design since the error mentions "~ design"?

Thanks very much for your help.

Session info

R version 4.1.1 (2021-08-10)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 18.04.6 LTS

Matrix products: default
BLAS/LAPACK: /opt/OpenBLAS/lib/libopenblasp-r0.3.3.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=en_US.UTF-8           LC_ADDRESS=en_US.UTF-8       
[10] LC_TELEPHONE=en_US.UTF-8      LC_MEASUREMENT=en_US.UTF-8    LC_IDENTIFICATION=en_US.UTF-8

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

other attached packages:
 [1] powsimR_1.2.5               gamlss.dist_6.0-3           MASS_7.3-54                 POWSC_1.10.0               
 [5] MAST_1.20.0                 RnaSeqSampleSize_2.12.0     RnaSeqSampleSizeData_1.34.0 edgeR_3.36.0               
 [9] Hmisc_4.7-1                 Formula_1.2-4               survival_3.2-11             lattice_0.20-44            
[13] sva_3.42.0                  genefilter_1.76.0           mgcv_1.8-36                 nlme_3.1-152               
[17] purrr_1.0.1                 muscat_1.8.2                reticulate_1.27             batchtools_0.9.15          
[21] zinbwave_1.16.0             EnhancedVolcano_1.12.0      broom_1.0.0                 tibble_3.2.1               
[25] clusterProfiler_4.2.2       pathfindR_1.6.3             pathfindR.data_1.1.2        DEsingle_1.14.0            
[29] vsn_3.62.0                  variancePartition_1.24.1    BiocParallel_1.28.3         limma_3.50.3               
[33] ggpubr_0.4.0                PCAtools_2.6.0              ggrepel_0.9.1               DESeq2_1.34.0              
[37] Matrix.utils_0.9.8          scDblFinder_1.8.0           pheatmap_1.0.12             scRNAseq_2.8.0             
[41] SingleR_1.8.1               biomaRt_2.50.3              org.Mm.eg.db_3.14.0         cowplot_1.1.1              
[45] gridExtra_2.3               kableExtra_1.3.4            scran_1.22.1                mvoutlier_2.1.1            
[49] sgeostat_1.0-27             RColorBrewer_1.1-3          ensembldb_2.18.4            AnnotationFilter_1.18.0    
[53] GenomicFeatures_1.46.5      AnnotationDbi_1.56.2        AnnotationHub_3.2.2         BiocFileCache_2.2.1        
[57] dbplyr_2.3.3                tidyr_1.3.0                 stringr_1.5.0               lubridate_1.9.0            
[61] timechange_0.1.1            Matrix_1.4-1                scater_1.22.0               ggplot2_3.4.4              
[65] scuttle_1.4.0               SingleCellExperiment_1.16.0 SummarizedExperiment_1.24.0 Biobase_2.54.0             
[69] GenomicRanges_1.46.1        GenomeInfoDb_1.30.1         IRanges_2.28.0              S4Vectors_0.32.4           
[73] BiocGenerics_0.40.0         MatrixGenerics_1.6.0        matrixStats_0.62.0          sp_1.5-0                   
[77] SeuratObject_4.1.0          Seurat_4.1.1                dendextend_1.16.0          

loaded via a namespace (and not attached):
  [1] abind_1.4-5                   SAVER_1.1.3                   ROTS_1.22.0                  
  [4] fastICA_1.2-3                 GO.db_3.14.0                  dqrng_0.3.0                  
  [7] affy_1.72.0                   RANN_2.6.1                    ellipsis_0.3.2               
 [10] memoise_2.0.1                 emmeans_1.8.0                 munsell_0.5.0                
 [13] scales_1.2.1                  grr_0.9.5                     locfit_1.5-9.6               
 [16] ggridges_0.5.3                segmented_1.6-0               xlsx_0.6.5                   
 [19] listenv_0.9.0                 blob_1.2.4                    interactiveDisplayBase_1.32.0
 [22] GOSemSim_2.20.0               fgsea_1.20.0                  quantreg_5.93                
 [25] nloptr_2.0.3                  truncnorm_1.0-9               DOSE_3.20.1                  
 [28] DECENT_1.1.1                  lme4_1.1-30                   sparseMatrixStats_1.6.0      
 [31] mclust_5.4.10                 jpeg_0.1-9                    iCOBRA_1.30.0                
 [34] htmltools_0.5.5               vipor_0.4.5                   doSNOW_1.0.20                
 [37] Rsamtools_2.10.0              progressr_0.13.0              ggplotify_0.1.0              
 [40] msir_1.3.3                    fastmatch_1.1-3               leiden_0.4.2                 
 [43] fastcluster_1.2.3             RUVSeq_1.28.0                 XML_3.99-0.10                
 [46] foreach_1.5.2                 aod_1.3.2                     GEOquery_2.70.0              
 [49] enrichplot_1.14.2             NBPSeq_0.3.1                  crayon_1.5.2                 
 [52] maps_3.4.0                    DelayedArray_0.20.0           tidyselect_1.2.0             
 [55] filelock_1.0.2                lpsymphony_1.30.0             withr_2.5.0                  
 [58] amap_0.8-19                   qlcMatrix_0.9.7               densityClust_0.3.2           
 [61] future.apply_1.11.0           DEoptimR_1.0-11               moments_0.14.1               
 [64] shiny_1.7.4.1                 snow_0.4-4                    ape_5.6-2                    
 [67] BiocManager_1.30.20           tzdb_0.4.0                    lmerTest_3.1-3               
 [70] RcppArmadillo_0.12.4.1.0      NOISeq_2.46.0                 Rdpack_2.3.1                 
 [73] SparseM_1.81                  multcomp_1.4-20               graphlayouts_0.8.0           
 [76] SCnorm_1.24.0                 pbkrtest_0.5.1                rappdirs_0.3.3               
 [79] circlize_0.4.15               doParallel_1.0.17             UpSetR_1.4.0                 
 [82] nonnest2_0.5-6                diptest_0.76-0                DBI_1.1.3                    
 [85] shape_1.4.6                   VGAM_1.1-7                    httr_1.4.6                   
 [88] spatstat.data_3.0-1           parallelly_1.36.0             xml2_1.3.5                   
 [91] DDRTree_0.1.5                 mnormt_2.1.1                  ZIM_1.1.0                    
 [94] deldir_1.0-6                  interp_1.1-3                  fastmap_1.1.1                
 [97] ExperimentHub_2.2.1           spatstat.geom_3.2-1           glue_1.6.2                   
[100] flexmix_2.3-18                tidygraph_1.2.1               rlang_1.1.1                  
[103] viridis_0.6.2                 rARPACK_0.11-0                bbmle_1.0.25                 
[106] maxLik_1.5-2                  labeling_0.4.2                plotly_4.10.0                
[109] gdata_2.19.0                  spatstat.sparse_3.0-1         clue_0.3-61                  
[112] arm_1.13-1                    mvtnorm_1.1-3                 cli_3.6.1                    
[115] zingeR_0.1.0                  minqa_1.2.4                   hierarchicell_1.0.0          
[118] fpc_2.2-9                     ash_1.0-15                    glmmTMB_1.1.4                
[121] latticeExtra_0.6-30           RCurl_1.98-1.7                openxlsx_4.2.5.2             
[124] polyclip_1.10-0               pillar_1.9.0                  tensorA_0.36.2               
[127] gplots_3.1.3                  prettyunits_1.1.1             R6_2.5.1                     
[130] ROCR_1.0-11                   bit64_4.0.5                   plyr_1.8.8                   
[133] ggstance_0.3.6                gtable_0.3.1                  estimability_1.4.1           
[136] xfun_0.39                     reshape2_1.4.4                restfulr_0.0.15              
[139] tweenr_1.0.2                  miniUI_0.1.1.1                gtools_3.9.3                 
[142] slam_0.1-50                   base64url_1.4                 scattermore_0.8              
[145] lifecycle_1.0.3               gmodels_2.18.1.1              splines_4.1.1                
[148] fdrtool_1.2.17                BSgenome_1.62.0               spatstat.core_2.4-4          
[151] KernSmooth_2.23-20            testthat_3.1.10               scatterpie_0.1.7             
[154] aroma.light_3.24.0            derfinderHelper_1.36.0        globals_0.16.2               
[157] sctransform_0.3.3             spatstat.utils_3.0-3          backports_1.4.1              
[160] viridisLite_0.4.1             utf8_1.2.3                    jsonlite_1.8.4               
[163] xlsxjars_0.6.1                blockmodeling_1.1.5           rpart_4.1-15                 
[166] GetoptLong_1.0.5              Rtsne_0.16                    prabclus_2.3-2               
[169] bayNorm_1.20.0                fitdistrplus_1.1-8            stringi_1.7.8                
[172] generics_0.1.3                GenomicFiles_1.38.0           ggfun_0.0.6                  
[175] cobs_1.3-5                    zlibbioc_1.40.0               htmlTable_2.4.1              
[178] brew_1.0-8                    EDASeq_2.28.0                 shinydashboard_0.7.2         
[181] hms_1.1.3                     png_0.1-8                     pbivnorm_0.6.0               
[184] ellipse_0.4.3                 DO.db_2.9                     coda_0.19-4                  
[187] pbapply_1.5-0                 rmarkdown_2.19                lazyeval_0.2.2               
[190] fields_15.2                   patchwork_1.1.2               numDeriv_2016.8-1.1          
[193] sandwich_3.0-2                htmlwidgets_1.6.2             annotate_1.72.0              
[196] scDD_1.26.0                   R.oo_1.25.0                   bluster_1.4.0                
[199] beachmat_2.10.0               BiocNeighbors_1.12.0          bumphunter_1.36.0            
[202] renv_0.15.5                   rbibutils_2.2.8               caTools_1.18.2               
[205] rsvd_1.0.5                    beeswarm_0.4.0                BiocIO_1.4.0                 
[208] ggforce_0.3.3                 zip_2.3.0                     R.methodsS3_1.8.2            
[211] spatstat.random_3.1-5         apcluster_1.4.11              fansi_1.0.4                  
[214] cluster_2.1.2                 RhpcBLASctl_0.21-247.1        bit_4.0.5                    
[217] Linnorm_2.26.0                rjson_0.2.21                  shadowtext_0.1.2             
[220] systemfonts_1.0.4             robustbase_0.95-0             knitr_1.43                   
[223] lavaan_0.6-17                 brio_1.1.3                    bdsmatrix_1.3-6              
[226] future_1.33.0                 IHW_1.30.0                    tools_4.1.1                  
[229] TMB_1.9.1                     data.table_1.14.8             RcppAnnoy_0.0.19             
[232] rhdf5filters_1.6.0            EBSeq_2.0.0                   DrImpute_1.0                 
[235] dotCall64_1.1-1               statmod_1.4.36                plotrix_3.8-2                
[238] GlobalOptions_0.1.2           qvalue_2.26.0                 Rcpp_1.0.11                  
[241] penalized_0.9-52              ica_1.0-3                     softImpute_1.4-1             
[244] RcppEigen_0.3.3.9.4           combinat_0.0-8                bitops_1.0-7                 
[247] quadprog_1.5-8                digest_0.6.33                 rngtools_1.5.2               
[250] downloader_0.4                Rhdf5lib_1.16.0               TH.data_1.1-1                
[253] yulab.utils_0.0.5             VariantAnnotation_1.40.0      ScaledMatrix_1.2.0           
[256] rstudioapi_0.15.0             BPSC_0.99.2                   parallel_4.1.1               
[259] XVector_0.34.0                magrittr_2.0.3                sparsesvd_0.2-2              
[262] svglite_2.1.0                 doRNG_1.8.2                   dplyr_1.1.2                  
[265] bayesm_3.1-6                  rhdf5_2.38.1                  ggbeeswarm_0.6.0             
[268] affyio_1.64.0                 geneplotter_1.72.0            gamlss_5.4-3                 
[271] CompQuadForm_1.4.3            ggraph_2.0.5                  modeltools_0.2-23            
[274] igraph_1.3.2                  Rttf2pt1_1.3.10               scPower_1.0.4                
[277] vctrs_0.6.3                   uwot_0.1.11                   zoo_1.8-12                   
[280] cachem_1.0.6                  Biostrings_2.62.0             colorspace_2.0-3             
[283] monocle_2.22.0                ShortRead_1.52.0              curl_5.0.1                   
[286] recount_1.28.0                httpuv_1.6.11                 carData_3.0-5                
[289] BiocVersion_3.14.0            GenomicAlignments_1.30.0      aplot_0.1.6                  
[292] gamlss.data_6.0-2             base64enc_0.1-3               class_7.3-19                 
[295] ProtGenerics_1.26.0           derfinder_1.36.0              DelayedMatrixStats_1.16.0    
[298] permute_0.9-7                 nnet_7.3-16                   ComplexHeatmap_2.10.0        
[301] pscl_1.5.5                    later_1.3.1                   extrafontdb_1.0              
[304] MatrixModels_0.5-0            hwriter_1.3.2.1               tensor_1.5                   
[307] DT_0.23                       spam_2.10-0                   kernlab_0.9-31               
[310] hexbin_1.28.3                 rgeos_0.5-9                   car_3.1-0                    
[313] xgboost_1.6.0.1               checkmate_2.1.0               rvest_1.0.3                  
[316] compiler_4.1.1                xtable_1.8-4                  Rmagic_2.0.3                 
[319] rJava_1.0-6                   farver_2.1.1                  extrafont_0.18               
[322] minpack.lm_1.2-4              codetools_0.2-18              rstatix_0.7.0                
[325] gridGraphics_0.5-1            evaluate_0.19                 yaml_2.3.6                   
[328] goftest_1.2-3                 rentrez_1.2.3                 preprocessCore_1.56.0        
[331] ggtree_3.2.1                  docopt_0.7.1                  mixtools_1.2.0               
[334] GenomeInfoDbData_1.2.7        RSpectra_0.16-1               promises_1.2.0.1             
[337] tidytree_0.3.9                RSQLite_2.3.1                 scone_1.26.0                 
[340] ggsignif_0.6.3                treeio_1.21.0                 FNN_1.1.3.1                  
[343] matlab_1.0.4                  lmtest_0.9-40                 BiocSingular_1.10.0          
[346] webshot_0.5.3                 baySeq_2.36.0                 heatmap3_1.1.9               
[349] vegan_2.6-2                   shinyBS_0.61.1                readr_2.1.4                  
[352] rtracklayer_1.54.0            boot_1.3-28                   metapod_1.2.0                
[355] R.utils_2.12.0                ggdendro_0.1.23               HSMMSingleCell_1.14.0        
[358] ggrastr_1.0.1                 KEGGREST_1.34.0               iterators_1.0.14             
[361] proj4_1.0-11                  blme_1.0-5                    ggalt_0.4.0                  
[364] progress_1.2.2                compositions_2.0-7            irlba_2.3.5                  
[367] foreign_0.8-81                mime_0.12                     miscTools_0.6-26             
[370] outliers_0.15                 pkgconfig_2.0.3