GabrielHoffman
commented
4 months ago Here is the issue and a fix: https://diseaseneurogenomics.github.io/dreamlet/articles/errors.html#errors-with-random-effects
Closed fengqlin closed 4 months ago
GabrielHoffman
commented
4 months ago Here is the issue and a fix: https://diseaseneurogenomics.github.io/dreamlet/articles/errors.html#errors-with-random-effects
Could this be a requirement for the matrix package version?
Matrix products: default
locale: [1] LC_COLLATE=en_US.UTF-8 LC_CTYPE=en_US.UTF-8 LC_MONETARY=en_US.UTF-8 LC_NUMERIC=C
[5] LC_TIME=en_US.UTF-8
time zone: Asia/Shanghai tzcode source: internal
attached base packages: [1] parallel stats4 tcltk stats graphics grDevices utils datasets methods base
other attached packages: [1] Matrix_1.6-1.1 variancePartition_1.33.0 BiocParallel_1.36.0
[4] doParallel_1.0.17 iterators_1.0.14 foreach_1.5.2
[7] pheatmap_1.0.12 broom_1.0.5 ClassDiscovery_3.4.5
[10] oompaBase_3.2.9 cluster_2.1.4 scatterplot3d_0.3-44
[13] factoextra_1.0.7 openxlsx_4.2.5.2 lubridate_1.9.3
[16] forcats_1.0.0 stringr_1.5.1 purrr_1.0.2
[19] readr_2.1.5 tidyverse_2.0.0 FactoMineR_2.9
[22] biomaRt_2.60.0 DESeq2_1.42.0 SummarizedExperiment_1.32.0 [25] MatrixGenerics_1.14.0 matrixStats_1.2.0 GenomicRanges_1.54.1
[28] GenomeInfoDb_1.40.1 IRanges_2.36.0 S4Vectors_0.40.2
[31] edgeR_4.0.16 limma_3.58.1 tibble_3.2.1
[34] tidyr_1.3.1 readxl_1.4.3 data.table_1.15.0
[37] units_0.8-5 Mfuzz_2.62.0 e1071_1.7-14
[40] treeio_1.26.0 pathview_1.42.0 BioEnricher_0.1.0
[43] DynDoc_1.80.0 Biobase_2.62.0 widgetTools_1.80.0
[46] ggbio_1.50.0 ggplot2_3.5.0 BiocGenerics_0.48.1
[49] dplyr_1.1.4 WGCNA_1.72-5 fastcluster_1.2.6
[52] dynamicTreeCut_1.63-1
loaded via a namespace (and not attached): [1] igraph_2.0.2 graph_1.80.0 Formula_1.2-5
[4] devtools_2.4.5 zlibbioc_1.48.0 tidyselect_1.2.0
[7] bit_4.0.5 clue_0.3-65 lattice_0.21-9
[10] rjson_0.2.21 urlchecker_1.0.1 blob_1.2.4
[13] S4Arrays_1.2.0 pbkrtest_0.5.2 dichromat_2.0-0.1
[16] png_0.1-8 cli_3.6.2 ggplotify_0.1.2
[19] ProtGenerics_1.36.0 askpass_1.2.0 openssl_2.1.1
[22] textshaping_0.3.7 BiocIO_1.12.0 shadowtext_0.1.3
[25] curl_5.2.0 mime_0.12 evaluate_0.23
[28] tidytree_0.4.6 ComplexHeatmap_2.18.0 stringi_1.8.4
[31] backports_1.4.1 lmerTest_3.1-3 XML_3.99-0.16.1
[34] httpuv_1.6.14 AnnotationDbi_1.64.1 magrittr_2.0.3
[37] clusterProfiler_4.12.0 rappdirs_0.3.3 leaps_3.1
[40] splines_4.3.2 mclust_6.1 ggraph_2.1.0
[43] org.Hs.eg.db_3.18.0 bcellViper_1.40.0 DT_0.32
[46] sessioninfo_1.2.2 progeny_1.26.0 DBI_1.2.2
[49] HDF5Array_1.30.1 corpcor_1.6.10 reactome.db_1.0.40
[52] withr_3.0.0 class_7.3-22 systemfonts_1.0.5
[55] rprojroot_2.0.4 enrichplot_1.22.0 RBGL_1.78.0
[58] GSEABase_1.64.0 tidygraph_1.3.1 rtracklayer_1.62.0
[61] BiocManager_1.30.22 htmlwidgets_1.6.4 fs_1.6.3
[64] SingleCellExperiment_1.24.0 triebeard_0.4.1 ggrepel_0.9.5
[67] labeling_0.4.3 fANCOVA_0.6-1 SparseArray_1.2.4
[70] cellranger_1.1.0 flashClust_1.01-2 annotate_1.80.0
[73] VariantAnnotation_1.48.1 zoo_1.8-12 GGally_2.2.1
[76] XVector_0.42.0 knitr_1.45 UCSC.utils_1.1.0
[79] RhpcBLASctl_0.23-42 gt_0.10.1 timechange_0.3.0
[82] fansi_1.0.6 caTools_1.18.2 patchwork_1.2.0
[85] grid_4.3.2 ggtree_3.10.0 rhdf5_2.46.1
[88] irlba_2.3.5.1 gridGraphics_0.5-1 ellipsis_0.3.2
[91] lazyeval_0.2.2 yaml_2.3.8 survival_3.5-7
[94] crayon_1.5.2 RColorBrewer_1.1-3 tweenr_2.0.3
[97] later_1.3.2 Rgraphviz_2.46.0 codetools_0.2-19
[100] base64enc_0.1-3 GlobalOptions_0.1.2 profvis_0.3.8
[103] aod_1.3.3 KEGGREST_1.36.0 shape_1.4.6.1
[106] ReactomePA_1.48.0 estimability_1.5 urltools_1.7.3
[109] Rsamtools_2.18.0 filelock_1.0.3 splitstackshape_1.4.8
[112] foreign_0.8-85 pkgconfig_2.0.3 KEGGgraph_1.62.0
[115] xml2_1.3.6 ggpubr_0.6.0 EnvStats_2.8.1
[118] GenomicAlignments_1.38.2 aplot_0.2.2 BSgenome_1.70.2
[121] ape_5.7-1 viridisLite_0.4.2 biovizBase_1.50.0
[124] xtable_1.8-4 car_3.1-2 plyr_1.8.9
[127] httr_1.4.7 rbibutils_2.2.16 tools_4.3.2
[130] pkgbuild_1.4.3 htmlTable_2.4.2 checkmate_2.3.1
[133] nlme_3.1-163 HDO.db_0.99.1 dbplyr_2.4.0
[136] lme4_1.1-35.1 digest_0.6.34 numDeriv_2016.8-1.1
[139] remaCor_0.0.18 farver_2.1.1 tzdb_0.4.0
[142] AnnotationFilter_1.26.0 reshape2_1.4.4 yulab.utils_0.1.4
[145] viridis_0.6.5 rpart_4.1.21 glue_1.7.0
[148] cachem_1.0.8 BiocFileCache_2.10.1 polyclip_1.10-6
[151] UpSetR_1.4.0 Hmisc_5.1-1 generics_0.1.3
[154] Biostrings_2.70.3 mvtnorm_1.2-4 pkgload_1.3.4
[157] statmod_1.5.0 impute_1.78.0 here_1.0.1
[160] ragg_1.2.7 ScaledMatrix_1.10.0 minqa_1.2.6
[163] carData_3.0-5 httr2_1.0.0 gson_0.1.0
[166] utf8_1.2.4 gtools_3.9.5 graphlayouts_1.1.0
[169] preprocessCore_1.64.0 ggsignif_0.6.4 gridExtra_2.3
[172] shiny_1.8.0 GSVA_1.50.1 GenomeInfoDbData_1.2.11
[175] rhdf5filters_1.14.1 RCurl_1.98-1.14 memoise_2.0.1
[178] rmarkdown_2.27 scales_1.3.0 europepmc_0.4.3
[181] Cairo_1.6-2 OrganismDbi_1.44.0 rstudioapi_0.15.0
[184] msigdbr_7.5.1 hms_1.1.3 munsell_0.5.0
[187] cowplot_1.1.3 colorspace_2.1-0 rlang_1.1.3
[190] HGNChelper_0.8.14 DelayedMatrixStats_1.24.0 sparseMatrixStats_1.14.0
[193] ggforce_0.4.2 circlize_0.4.16 xfun_0.42
[196] multcompView_0.1-9 coda_0.19-4.1 TH.data_1.1-2
[199] remotes_2.5.0 tkWidgets_1.80.0 emmeans_1.10.0
[202] abind_1.4-5 GOSemSim_2.28.1 Rhdf5lib_1.24.2
[205] Rdpack_2.6 bitops_1.0-7 promises_1.2.1
[208] scatterpie_0.2.1 RSQLite_2.3.5 qvalue_2.34.0
[211] sandwich_3.1-0 fgsea_1.28.0 DelayedArray_0.28.0
[214] proxy_0.4-27 GO.db_3.18.0 compiler_4.3.2
[217] prettyunits_1.2.0 boot_1.3-28.1 beachmat_2.18.1
[220] graphite_1.46.0 Rcpp_1.0.12 BiocSingular_1.18.0
[223] usethis_2.2.3 MASS_7.3-60 progress_1.2.3
[226] babelgene_22.9 R6_2.5.1 fastmap_1.1.1
[229] multcomp_1.4-25 fastmatch_1.1-4 rstatix_0.7.2
[232] ensembldb_2.26.0 ggstats_0.5.1 rsvd_1.0.5
[235] nnet_7.3-19 gtable_0.3.4 KernSmooth_2.23-22
[238] miniUI_0.1.1.1 htmltools_0.5.7 bit64_4.0.5
[241] lifecycle_1.0.4 zip_2.3.1 oompaData_3.1.4
[244] dorothea_1.16.0 nloptr_2.0.3 restfulr_0.0.15
[247] sass_0.4.8 vctrs_0.6.5 DOSE_3.28.2
[250] ggfun_0.1.4 pillar_1.9.0 gplots_3.1.3.1
[253] GenomicFeatures_1.54.3 magick_2.8.3 locfit_1.5-9.8
[256] jsonlite_1.8.8 GetoptLong_1.0.5