search

GabrielHoffman / variancePartition

Quantify and interpret divers of variation in multilevel gene expression experiments
http://gabrielhoffman.github.io/variancePartition/
60 stars 14 forks source link

Error in checkModelStatus(fitInit, showWarnings = showWarnings, colinearityCutoff = colinearityCutoff) : boundary (singular) fit: see help('isSingular') #77

Closed Jason-bot-stack closed 1 year ago

Jason-bot-stack commented 1 year ago

When I run fitExtractVarPartModel, I get the following error： boundary (singular) fit: see help('isSingular') boundary (singular) fit: see help('isSingular') Error in checkModelStatus(fitInit, showWarnings = showWarnings, colinearityCutoff = colinearityCutoff) : boundary (singular) fit: see help('isSingular')

head(info) SampleID Organ Individual
LC210124182 LC210124182 L Sow LC210124006 LC210124006 L F LC210124186 LC210124186 L S LC210124080 LC210124080 L F LC210525032X1 LC210525032X1 L S LC210124188 LC210124188 L S

Expr[1:3,1:6] LC210525007 LC210525044 LC210124047 LC210124181 LC210525005 B_1 0.0010860871 0.004464895 0.05240251 0.109779263 7.868653e-05 B_2 0.0492892909 0.226155744 0.00000000 0.002305179 5.246474e-03 B_3 0.0005413335 0.009890745 0.03734855 0.120320965 0.000000e+00 LC210525030 B_1 0.00000000 B_2 0.00180864 B_3 0.00000000 form <- ~ (1|Individual) + (1|Organ) varPart <- fitExtractVarPartModel( Expr2, form, info ) boundary (singular) fit: see help('isSingular') boundary (singular) fit: see help('isSingular') Error in checkModelStatus(fitInit, showWarnings = showWarnings, colinearityCutoff = colinearityCutoff) : boundary (singular) fit: see help('isSingular')

sessionInfo() R version 4.0.3 (2020-10-10) Platform: x86_64-conda-linux-gnu (64-bit) Running under: CentOS Linux 7 (Core)

Matrix products: default BLAS/LAPACK: /home/aihsh/miniconda3/envs/r403/lib/libopenblasp-r0.3.12.so

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

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

other attached packages: [1] lme4_1.1-29 Matrix_1.5-4 variancePartition_1.20.0 [4] Biobase_2.50.0 BiocGenerics_0.36.1 scales_1.2.1
[7] BiocParallel_1.24.1 limma_3.46.0 forcats_0.5.1
[10] stringr_1.5.0 dplyr_1.1.2 purrr_1.0.1
[13] readr_2.1.2 tidyr_1.3.0 tibble_3.2.1
[16] ggplot2_3.4.2 tidyverse_1.3.1

loaded via a namespace (and not attached): [1] httr_1.4.6 jsonlite_1.8.4 splines_4.0.3 foreach_1.5.2
[5] modelr_0.1.8 gtools_3.9.4 cellranger_1.1.0 progress_1.2.2
[9] pillar_1.9.0 backports_1.4.1 lattice_0.20-45 glue_1.6.2
[13] rvest_1.0.2 minqa_1.2.4 colorspace_2.1-0 plyr_1.8.8
[17] pkgconfig_2.0.3 broom_0.8.0 haven_2.5.0 tzdb_0.3.0
[21] generics_0.1.3 withr_2.5.0 pbkrtest_0.5.1 cli_3.6.1
[25] magrittr_2.0.3 crayon_1.5.2 readxl_1.4.1 fs_1.6.2
[29] fansi_1.0.4 doParallel_1.0.17 nlme_3.1-153 MASS_7.3-54
[33] gplots_3.1.3 xml2_1.3.4 tools_4.0.3 prettyunits_1.1.1 [37] hms_1.1.3 lifecycle_1.0.3 munsell_0.5.0 reprex_2.0.1
[41] colorRamps_2.3.1 compiler_4.0.3 caTools_1.18.2 rlang_1.1.1
[45] grid_4.0.3 nloptr_1.2.2.3 iterators_1.0.14 rstudioapi_0.13
[49] bitops_1.0-7 boot_1.3-28 gtable_0.3.3 codetools_0.2-18
[53] DBI_1.1.3 reshape2_1.4.4 R6_2.5.1 lubridate_1.8.0
[57] utf8_1.2.3 KernSmooth_2.23-20 stringi_1.7.12 Rcpp_1.0.10
[61] vctrs_0.6.2 dbplyr_2.3.2 tidyselect_1.2.0