limma not working correctly
chengmingbo opened this issue · 2 comments
chengmingbo commented
Hi, limma looks still not working.
Here I used ifnb data to create fake replicates. EdgeR works fine, but limma not.
The R code
library(SeuratData)
library(Seurat)
library(Libra)
InstallData("ifnb")
LoadData("ifnb")
ifnb <- UpdateSeuratObject(ifnb)
ifnb$celltype <- as.character(ifnb$seurat_annotations)
ifnb$rep <- ifnb$orig.ident
lenctrl = length(which(ifnb$rep=="IMMUNE_CTRL"))
lenstim = length(which(ifnb$rep=="IMMUNE_STIM"))
ifnb$rep[ifnb$rep=="IMMUNE_CTRL"] <-paste0("ctrl_", c(rep(1, as.integer(lenctrl/2)),rep(2, lenctrl-as.integer(lenctrl/2))))
ifnb$rep[ifnb$rep=="IMMUNE_STIM"] <-paste0("stim_", c(rep(1, as.integer(lenstim/2)),rep(2, lenstim-as.integer(lenstim/2))))
DE = run_de(ifnb, cell_type_col = "celltype", label_col = "stim", replicate_col="rep", de_method="limma")Error message:
[1] "B"
[1] "B Activated"
[1] "CD14 Mono"
[1] "CD16 Mono"
[1] "CD4 Memory T"
[1] "CD4 Naive T"
[1] "CD8 T"
[1] "DC"
[1] "Eryth"
[1] "Mk"
[1] "NK"
[1] "pDC"
[1] "T activated"
object 'trend_bool' not foundobject 'trend_bool' not foundobject 'trend_bool' not foundobject 'trend_bool' not foundobject 'trend_bool' not foundobject 'trend_bool' not foundobject 'trend_bool' not foundobject 'trend_bool' not foundobject 'trend_bool' not foundobject 'trend_bool' not foundobject 'trend_bool' not foundobject 'trend_bool' not foundobject 'trend_bool' not foundError: Problem with `mutate()` column `p_val_adj`.
ℹ `p_val_adj = p.adjust(p_val, method = "BH")`.
✖ object 'p_val' not found
Run `rlang::last_error()` to see where the error occurred.Session info
r$> sessionInfo()
R version 4.1.0 (2021-05-18)
Platform: x86_64-conda-linux-gnu (64-bit)
Running under: Rocky Linux 8.5 (Green Obsidian)
Matrix products: default
BLAS/LAPACK: /data/sz753404/miniconda3/envs/schema/lib/libopenblasp-r0.3.17.so
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=de_DE.UTF-8 LC_COLLATE=en_US.UTF-8 LC_MONETARY=de_DE.UTF-8
[6] LC_MESSAGES=en_US.UTF-8 LC_PAPER=de_DE.UTF-8 LC_NAME=C LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=de_DE.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] ifnb.SeuratData_3.1.0 bmcite.SeuratData_0.3.0 SeuratData_0.2.1 Libra_1.0.0 SeuratObject_4.0.4 Seurat_4.0.6
loaded via a namespace (and not attached):
[1] blme_1.0-5 plyr_1.8.6 igraph_1.3.0 lazyeval_0.2.2 TMB_1.8.1
[6] splines_4.1.0 BiocParallel_1.26.2 listenv_0.8.0 scattermore_0.7 TH.data_1.1-0
[11] GenomeInfoDb_1.28.4 ggplot2_3.3.5 digest_0.6.29 htmltools_0.5.2 lmerTest_3.1-3
[16] fansi_0.5.0 magrittr_2.0.1 memoise_2.0.1 tensor_1.5 cluster_2.1.2
[21] ROCR_1.0-11 limma_3.48.3 globals_0.14.0 Biostrings_2.60.2 annotate_1.70.0
[26] tester_0.1.7 matrixStats_0.61.0 sandwich_3.0-1 spatstat.sparse_2.1-0 colorspace_2.0-2
[31] rappdirs_0.3.3 blob_1.2.2 ggrepel_0.9.1 dplyr_1.0.7 crayon_1.4.2
[36] RCurl_1.98-1.5 jsonlite_1.7.2 genefilter_1.74.1 lme4_1.1-27.1 spatstat.data_2.1-2
[41] survival_3.2-13 zoo_1.8-9 glue_1.6.0 polyclip_1.10-0 gtable_0.3.0
[46] emmeans_1.7.0 zlibbioc_1.38.0 XVector_0.32.0 leiden_0.3.9 DelayedArray_0.18.0
[51] future.apply_1.8.1 BiocGenerics_0.38.0 abind_1.4-5 scales_1.1.1 mvtnorm_1.1-3
[56] DBI_1.1.2 edgeR_3.34.1 miniUI_0.1.1.1 Rcpp_1.0.7 viridisLite_0.4.0
[61] xtable_1.8-4 reticulate_1.22 spatstat.core_2.3-2 bit_4.0.4 stats4_4.1.0
[66] htmlwidgets_1.5.4 httr_1.4.2 RColorBrewer_1.1-2 ellipsis_0.3.2 ica_1.0-2
[71] pkgconfig_2.0.3 XML_3.99-0.8 uwot_0.1.11 deldir_1.0-6 locfit_1.5-9.4
[76] utf8_1.2.2 tidyselect_1.1.1 rlang_0.4.12 reshape2_1.4.4 later_1.3.0
[81] AnnotationDbi_1.54.1 pbmcapply_1.5.1 munsell_0.5.0 tools_4.1.0 cachem_1.0.6
[86] cli_3.1.0 generics_0.1.1 RSQLite_2.2.8 ggridges_0.5.3 stringr_1.4.0
[91] fastmap_1.1.0 goftest_1.2-3 bit64_4.0.5 fitdistrplus_1.1-6 purrr_0.3.4
[96] RANN_2.6.1 KEGGREST_1.32.0 pbapply_1.5-0 future_1.23.0 nlme_3.1-153
[101] mime_0.12 compiler_4.1.0 plotly_4.10.0 png_0.1-7 spatstat.utils_2.3-0
[106] tibble_3.1.6 geneplotter_1.70.0 stringi_1.7.5 forcats_0.5.1 lattice_0.20-45
[111] Matrix_1.3-4 nloptr_1.2.2.3 vctrs_0.3.8 pillar_1.6.4 lifecycle_1.0.1
[116] spatstat.geom_2.4-0 lmtest_0.9-39 estimability_1.3 RcppAnnoy_0.0.19 data.table_1.14.2
[121] cowplot_1.1.1 bitops_1.0-7 irlba_2.3.5 httpuv_1.6.4 patchwork_1.1.1
[126] GenomicRanges_1.44.0 R6_2.5.1 promises_1.2.0.1 KernSmooth_2.23-20 gridExtra_2.3
[131] IRanges_2.26.0 parallelly_1.30.0 codetools_0.2-18 boot_1.3-28 MASS_7.3-54
[136] assertthat_0.2.1 SummarizedExperiment_1.22.0 DESeq2_1.32.0 sctransform_0.3.2 multcomp_1.4-17
[141] S4Vectors_0.30.2 GenomeInfoDbData_1.2.6 mgcv_1.8-38 parallel_4.1.0 grid_4.1.0
[146] rpart_4.1-15 coda_0.19-4 glmmTMB_1.1.3 tidyr_1.1.4 minqa_1.2.4
[151] MatrixGenerics_1.4.3 Rtsne_0.15 numDeriv_2016.8-1.1 Biobase_2.52.0 shiny_1.7.1 chengmingbo commented
toy data failed too.
DE = run_de(hagai_toy, cell_type_col = "cell_type", label_col = "label", replicate_col="replicate", de_method="limma")[1] "bone marrow derived mononuclear phagocytes"
object 'trend_bool' not foundError: Problem with `mutate()` column `p_val_adj`.
ℹ `p_val_adj = p.adjust(p_val, method = "BH")`.
✖ object 'p_val' not found
Run `rlang::last_error()` to see where the error occurred.jordansquair commented
pushed a fix.