Closed se2cheeese closed 2 years ago
Can you provide sessionInfo(). Thanks
From: se2cheeese @.> Sent: Friday, May 13, 2022 1:42:30 AM To: GabrielHoffman/variancePartition @.> Cc: Subscribed @.***> Subject: [GabrielHoffman/variancePartition] boundary (singular) fit: see help('isSingular') (Issue #53)
USE CAUTION: External Message.
Hi, thank you for this great tool. It was working well with my data until a few days ago, but now even when I run the codes in your vignettes for a test, the following message shows up.
param = SnowParam(4, "SOCK", progressbar=TRUE)
form <- ~ Disease + (1|Individual)
vobjDream = voomWithDreamWeights( geneExpr, form, metadata, BPPARAM=param )
fitmm = dream(vobjDream, form, metadata ) fitmm = eBayes(fitmm)
Memory usage to store result: >2.4 Mb
Dividing work into 50 chunks...
iteration: 1 boundary (singular) fit: see help('isSingular') boundary (singular) fit: see help('isSingular') boundary (singular) fit: see help('isSingular') boundary (singular) fit: see help('isSingular') boundary (singular) fit: see help('isSingular') boundary (singular) fit: see help('isSingular') boundary (singular) fit: see help('isSingular') boundary (singular) fit: see help('isSingular') boundary (singular) fit: see help('isSingular') boundary (singular) fit: see help('isSingular')
�2 boundary (singular) fit: see help('isSingular') boundary (singular) fit: see help('isSingular') boundary (singular) fit: see help('isSingular') boundary (singular) fit: see help('isSingular') boundary (singular) fit: see help('isSingular') boundary (singular) fit: see help('isSingular') boundary (singular) fit: see help('isSingular')
Could you help tackle this problem? Appreciate.
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Thank you for a quick response. This is the sessionInfo() for the test (codes from vignettes).
R version 4.0.0 (2020-04-24)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)
Matrix products: default
BLAS: /opt/applications/R/4.0.0/gnu/lib64/R/lib/libRblas.so
LAPACK: /opt/applications/R/4.0.0/gnu/lib64/R/lib/libRlapack.so
locale:
[1] LC_CTYPE=en_US.utf8 LC_NUMERIC=C
[3] LC_TIME=en_US.utf8 LC_COLLATE=en_US.utf8
[5] LC_MONETARY=en_US.utf8 LC_MESSAGES=en_US.utf8
[7] LC_PAPER=en_US.utf8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.utf8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] edgeR_3.30.3 variancePartition_1.25.4 BiocParallel_1.24.1
[4] limma_3.46.0 ggplot2_3.3.6
loaded via a namespace (and not attached):
[1] Biobase_2.50.0 tidyr_1.2.0 jsonlite_1.8.0
[4] splines_4.0.0 foreach_1.5.2 RhpcBLASctl_0.21-247.1
[7] gtools_3.9.2 Rdpack_2.1.3 assertthat_0.2.1
[10] progress_1.2.2 pillar_1.7.0 backports_1.4.1
[13] lattice_0.20-45 glue_1.6.2 uuid_1.1-0
[16] digest_0.6.29 rbibutils_2.2.7 minqa_1.2.4
[19] colorspace_2.0-3 htmltools_0.5.2 Matrix_1.4-1
[22] plyr_1.8.7 pkgconfig_2.0.3 broom_0.8.0
[25] purrr_0.3.4 snow_0.4-4 scales_1.2.0
[28] lme4_1.1-29 tibble_3.1.7 generics_0.1.2
[31] ellipsis_0.3.2 withr_2.5.0 repr_1.1.4
[34] BiocGenerics_0.36.1 pbkrtest_0.5.1 cli_3.3.0
[37] magrittr_2.0.3 crayon_1.5.1 evaluate_0.15
[40] fansi_1.0.3 doParallel_1.0.17 nlme_3.1-157
[43] MASS_7.3-57 gplots_3.1.3 tools_4.0.0
[46] prettyunits_1.1.1 hms_1.1.1 lifecycle_1.0.1
[49] stringr_1.4.0 munsell_0.5.0 locfit_1.5-9.4
[52] aod_1.3.2 compiler_4.0.0 caTools_1.18.2
[55] rlang_1.0.2 grid_4.0.0 nloptr_2.0.1
[58] pbdZMQ_0.3-7 iterators_1.0.14 IRkernel_1.2
[61] bitops_1.0-7 base64enc_0.1-3 boot_1.3-28
[64] gtable_0.3.0 codetools_0.2-18 DBI_1.1.2
[67] reshape2_1.4.4 R6_2.5.1 dplyr_1.0.9
[70] fastmap_1.1.0 utf8_1.2.2 KernSmooth_2.23-20
[73] stringi_1.7.6 parallel_4.0.0 IRdisplay_1.1
[76] Rcpp_1.0.8.3 vctrs_0.4.1 tidyselect_1.1.2
And this is the sessionInfo() for my data which ended up with the error.
R version 4.0.0 (2020-04-24)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)
Matrix products: default
BLAS: /opt/applications/R/4.0.0/gnu/lib64/R/lib/libRblas.so
LAPACK: /opt/applications/R/4.0.0/gnu/lib64/R/lib/libRlapack.so
locale:
[1] LC_CTYPE=en_US.utf8 LC_NUMERIC=C
[3] LC_TIME=en_US.utf8 LC_COLLATE=en_US.utf8
[5] LC_MONETARY=en_US.utf8 LC_MESSAGES=en_US.utf8
[7] LC_PAPER=en_US.utf8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.utf8 LC_IDENTIFICATION=C
attached base packages:
[1] grid stats4 parallel stats graphics grDevices utils
[8] datasets methods base
other attached packages:
[1] robustbase_0.95-0 ComplexHeatmap_2.4.3 DT_0.23
[4] data.table_1.14.2 fgsea_1.14.0 RCy3_2.8.1
[7] GSA_1.03.1 RCurl_1.98-1.6 spatstat_2.3-4
[10] spatstat.linnet_2.3-2 spatstat.core_2.4-2 rpart_4.1.16
[13] spatstat.random_2.2-0 spatstat.geom_2.4-0 spatstat.data_2.2-0
[16] bigutilsr_0.3.4 GEOquery_2.56.0 PCAtools_2.0.0
[19] cowplot_1.1.1 lattice_0.20-45 reshape2_1.4.4
[22] ggrepel_0.9.1 rafalib_1.0.0 matrixStats_0.62.0
[25] preprocessCore_1.50.0 org.Hs.eg.db_3.11.4 GO.db_3.11.4
[28] AnnotationDbi_1.52.0 IRanges_2.24.1 S4Vectors_0.28.1
[31] NMF_0.24.0 bigmemory_4.6.1 Biobase_2.50.0
[34] BiocGenerics_0.36.1 cluster_2.1.3 rngtools_1.5.2
[37] pkgmaker_0.32.2 registry_0.5-1 gplots_3.1.3
[40] variancePartition_1.25.4 Glimma_1.16.0 RColorBrewer_1.1-3
[43] BatchQC_1.16.3 forcats_0.5.1 stringr_1.4.0
[46] dplyr_1.0.9 purrr_0.3.4 readr_2.1.2
[49] tidyr_1.2.0 tibble_3.1.7 tidyverse_1.3.1
[52] UpSetR_1.4.0 edgeR_3.30.3 limma_3.46.0
[55] gridExtra_2.3 ggplot2_3.3.6 sva_3.36.0
[58] BiocParallel_1.24.1 genefilter_1.76.0 mgcv_1.8-40
[61] nlme_3.1-157
loaded via a namespace (and not attached):
[1] SparseM_1.81 pbdZMQ_0.3-7
[3] R.methodsS3_1.8.1 coda_0.19-4
[5] bit64_4.0.5 knitr_1.37
[7] irlba_2.3.5 DelayedArray_0.14.1
[9] R.utils_2.11.0 doParallel_1.0.17
[11] generics_0.1.2 snow_0.4-4
[13] RhpcBLASctl_0.21-247.1 RSQLite_2.2.14
[15] bit_4.0.4 tzdb_0.3.0
[17] webshot_0.5.3 xml2_1.3.3
[19] lubridate_1.8.0 httpuv_1.6.5
[21] assertthat_0.2.1 viridis_0.6.2
[23] xfun_0.29 hms_1.1.1
[25] evaluate_0.15 promises_1.2.0.1
[27] TSP_1.1-11 DEoptimR_1.0-10
[29] fansi_1.0.3 progress_1.2.2
[31] caTools_1.18.2 dendextend_1.15.2
[33] dbplyr_2.1.1 readxl_1.4.0
[35] igraph_1.3.1 DBI_1.1.2
[37] htmlwidgets_1.5.4 mcmc_0.9-7
[39] ellipsis_0.3.2 RSpectra_0.16-1
[41] backports_1.4.1 annotate_1.68.0
[43] MCMCpack_1.6-3 aod_1.3.2
[45] gridBase_0.4-7 moments_0.14
[47] deldir_1.0-6 vctrs_0.4.1
[49] Cairo_1.5-15 quantreg_5.93
[51] abind_1.4-5 cachem_1.0.6
[53] withr_2.5.0 prettyunits_1.1.1
[55] goftest_1.2-3 IRdisplay_1.1
[57] lazyeval_0.2.2 crayon_1.5.1
[59] labeling_0.4.2 pkgconfig_2.0.3
[61] seriation_1.3.0 rlang_1.0.2
[63] RJSONIO_1.3-1.6 lifecycle_1.0.1
[65] MatrixModels_0.5-0 bigmemory.sri_0.1.3
[67] modelr_0.1.8 rsvd_1.0.5
[69] cellranger_1.1.0 polyclip_1.10-0
[71] graph_1.66.0 Matrix_1.4-1
[73] IRkernel_1.2 boot_1.3-28
[75] reprex_2.0.1 base64enc_0.1-3
[77] GlobalOptions_0.1.2 rjson_0.2.21
[79] png_0.1-7 viridisLite_0.4.0
[81] bitops_1.0-7 R.oo_1.24.0
[83] KernSmooth_2.23-20 pander_0.6.5
[85] blob_1.2.3 DelayedMatrixStats_1.10.1
[87] shape_1.4.6 ggvis_0.4.7
[89] scales_1.2.0 memoise_2.0.1
[91] magrittr_2.0.3 plyr_1.8.7
[93] compiler_4.0.0 dqrng_0.3.0
[95] clue_0.3-60 lme4_1.1-29
[97] cli_3.3.0 lmerTest_3.1-3
[99] MASS_7.3-57 tidyselect_1.1.2
[101] stringi_1.7.6 BiocSingular_1.4.0
[103] locfit_1.5-9.4 fastmatch_1.1-3
[105] tools_4.0.0 bigassertr_0.1.5
[107] circlize_0.4.14 rstudioapi_0.13
[109] uuid_1.1-0 foreach_1.5.2
[111] farver_2.1.0 digest_0.6.29
[113] shiny_1.7.1 Rcpp_1.0.8.3
[115] broom_0.8.0 later_1.3.0
[117] httr_1.4.3 Rdpack_2.1.3
[119] colorspace_2.0-3 rvest_1.0.2
[121] XML_3.99-0.9 fs_1.5.2
[123] tensor_1.5 splines_4.0.0
[125] spatstat.utils_2.3-1 plotly_4.10.0
[127] xtable_1.8-4 jsonlite_1.8.0
[129] nloptr_2.0.1 heatmaply_1.3.0
[131] corpcor_1.6.10 R6_2.5.1
[133] pillar_1.7.0 htmltools_0.5.2
[135] mime_0.12 glue_1.6.2
[137] fastmap_1.1.0 minqa_1.2.4
[139] codetools_0.2-18 pcaPP_2.0-1
[141] mvtnorm_1.1-3 utf8_1.2.2
[143] spatstat.sparse_2.1-1 numDeriv_2016.8-1.1
[145] pbkrtest_0.5.1 gtools_3.9.2
[147] survival_3.3-1 rmarkdown_2.14
[149] repr_1.1.4 munsell_0.5.0
[151] GetoptLong_1.0.5 iterators_1.0.14
[153] haven_2.5.0 gtable_0.3.0
[155] rbibutils_2.2.7
This has been fixed in variancePartition v1.25.13
. See notes
(https://gabrielhoffman.github.io/variancePartition/news/index.html#variancepartition-12513)
Try reinstalling following instructions here: https://gabrielhoffman.github.io/variancePartition/index.html
Thank you very much. We followed your instruction and confirmed that it works well after reinstallation.
Hi, thank you for this great tool. It was working well with my data until a few days ago, but now even when I run the codes in your vignettes for a test, the following message shows up.
The variable to be tested must be a fixed effect
form <- ~ Disease + (1|Individual)
estimate weights using linear mixed model of dream
vobjDream = voomWithDreamWeights( geneExpr, form, metadata, BPPARAM=param )
Fit the dream model on each gene
By default, uses the Satterthwaite approximation for the hypothesis test
fitmm = dream(vobjDream, form, metadata ) fitmm = eBayes(fitmm)
Memory usage to store result: >2.4 Mb
Dividing work into 50 chunks...
iteration: 1 boundary (singular) fit: see help('isSingular') boundary (singular) fit: see help('isSingular') boundary (singular) fit: see help('isSingular') boundary (singular) fit: see help('isSingular') boundary (singular) fit: see help('isSingular') boundary (singular) fit: see help('isSingular') boundary (singular) fit: see help('isSingular') boundary (singular) fit: see help('isSingular') boundary (singular) fit: see help('isSingular') boundary (singular) fit: see help('isSingular')
2 boundary (singular) fit: see help('isSingular') boundary (singular) fit: see help('isSingular') boundary (singular) fit: see help('isSingular') boundary (singular) fit: see help('isSingular') boundary (singular) fit: see help('isSingular') boundary (singular) fit: see help('isSingular') boundary (singular) fit: see help('isSingular')
fitmm = dream(vobjDream, form, m, BPPARAM=param) fitmm = eBayes(fitmm)
boundary (singular) fit: see help('isSingular')
Error in run_model_check_mixed(fit, showWarnings, dream, colinearityCutoff, : boundary (singular) fit: see help('isSingular') Traceback: