PercentageFeatureSet() error

[Changfei6]

when i use sc[["percent_MT"]] <- PercentageFeatureSet(sc, pattern = "^MT-|^mt-"), I get the error Error : Error in LayerData(): ! features must be one of "RPL22", "PARK7", "ENO1", "HP1BP3", "CDC42", "RPL11", "SRSF10", "SRRM1", "RSRP1", "SH3BGRL3", "WASF2", "ATP5IF1", "PTP4A2", "SFPQ", "NDUFS5", "MACF1", "YBX1", "RPS8", "PRDX1", "UQCRH", "TMEM59", "JUN", "JAK1", "SERBP1", "SRSF11", "GNG5", "RPL5", "CSDE1", "ATP1A1", "TXNIP", "MCL1", "S100A10", "S100A11", "S100A6", "S100A4", "RPS27", "TPM3", "ASH1L", "SSR2", "LMNA", "TAGLN2", "MGST3", "ATP1B1", "PRRC2C", "GLUL", "ARPC5", "TPR", "ELF3", "BTG2", "NUCKS1", "CD55", "CD46", "ATF3", "H3F3A", "ARF1", "GUK1", "TOMM20", "ARID4B", "HNRNPU", "RPS7", "LAPTM4A", "RHOB", "OST4", "FOSL2", "PPP1CB", "SRSF7", "ZFP36L2", "CALM2", "SPTBN1", "RTN4", "RPS27A", "REL", "ACTR2", "ANXA4", "PCBP1", "TMSB10", "TGOLN2", "COX5B", "EIF5B", "RPL31", "GCC2", "DBI", "MZT2B", "UBXN4", "PPIG", "ATP5MC3", "HNRNPA3", "NFE2L2", "COL3A1", "SF3B1", "HSPD1", "HSPE1", "BZW1", "CFLAR", "EEF1B2", "RPL37A", "ARPC2", "NCL", "PTMA", "LRRFIP1", "SEPT2", "RPL32", "RPL15", "GOLGA4", "RPSA", "RPL14", "NKTR", "TMA7", "RHOA", "RPL29", "SPCS1", "ARL6IP5", "FOXP1", "MTRNR2L12", "RPL24", "ZBTB20", "GOLGB1", "CNBP", "CDV3", "ATP1B3", "TM4SF1", "SERP1", "MBNL1", "CCNL1", "SEC62", "SKIL", "EIF4A2", "LPP", "RPL35A", "ATP5ME", "RPL9", "IGFBP7", "CCNI", "HNRNPDL", "SPARCL1", "H2AFZ", "UBE2D3", "RPL34", "ANXA5", "RPS3A", "SUB1", "RPL37", "GPBP1", "BTF3", "TBCA", "RPS23", "COX7C", "CAST", "HINT1", "UQCRQ", "SKP1", "UBE2B", "DDX46", "EGR1", "CYSTM1", "CSNK1A1", "CD74", "RPS14", "SPARC", "NPM1", "DUSP1", "ATP6V0E1", "HNRNPAB", "HNRNPH1", "CANX", "SQSTM1", "RACK1", "DEK", "HLA-A", "HLA-E", "IER3", "HLA-C", "HLA-B", "CLIC1", "HSPA1A", "RPS18", "RPL10A", "SRSF3", "HSP90AB1", "DST", "EEF1A1", "COX7A2", "PNRC1", "PNISR", "CD164", "RPS12", "EZR", "SOD2", "ACTB", "RAC1", "NDUFA4", "TOMM7", "HNRNPA2B1", "TAX1BP1", "SEPT7", "PPIA", "SEC61G", "CHCHD2", "GTF2I", "HSPB1", "AKAP9", "FAM133B", "COL1A2", "SEM1", "BRI3", "KMT2E", "NAMPT", "CALD1", "NDUFB2", "DNAJB6", "SLC25A6", "CD99", "TMSB4X", "EIF1AX", "SAT1", "DDX3X", "TIMP1", "RBM3", "RPS4X", "ATRX", "COX7B", "TSC22D3", "RPL39", "SSR4", "RPL10", "CTSB", "SARAF", "TACC1", "CEBPD", "RPS20", "SDCBP", "RAB2A", "TRAM1", "RPL7", "UQCRB", "MTDH", "RPL30", "COX6C", "PABPC1", "YWHAZ", "ZNF706", "EIF3E", "LY6E", "EEF1D", "RPL8", "NFIB", "RPS6", "DNAJA1", "CLTA", "ZFAND5", "ANXA1", "HNRNPK", "SEC61B", "TXN", "ATP6V1G1", "GSN", "RPL35", "HSPA5", "RPL12", "LCN2", "SET", "RPL7A", "EDF1", "TUBB4B", "IFITM2", "IFITM3", "RPLP2", "CD151", "POLR2L", "CTSD", "CD81", "KCNQ1OT1", "RPL27A", "MTRNR2L8", "EIF4G2", "C11orf58", "RPS13", "LDHA", "CD59", "CD44", "FTH1", "AHNAK", "COX8A", "FKBP2", "PRDX5", "SF1", "FAU", "NEAT1", "MALAT1", "CFL1", "GSTP1", "SPCS2", "RPS3", "TAF1D", "NNMT", "ATP5MG", "RPS25", "HSPA8", "APLP2", "KLF6", "VIM", "KIF5B", "ITGB1", "JMJD1C", "DDX21", "SRGN", "PPA1", "PSAP", "DDIT4", "RPS24", "TM9SF3", "ATP5MD", "EIF3A", "CD9", "GAPDH", "TPI1", "C12orf57", "YBX3", "EMP1", "MGP", "SCAF11", "SLC38A2", "TUBA1B", "TMBIM6", "LIMA1", "NR4A1", "KRT8", "PFDN5", "PCBP2", "ATP5MC2", "HNRNPA1", "CD63", "RPS26", "RPL41", "MYL6", "PTGES3", "NACA", "RAP1B", "LYZ", "TSPAN8", "NAP1L1", "LUM", "DCN", "BTG1", "SLC25A3", "HSP90B1", "ARPC3", "RPL6", "PEBP1", "RPLP0", "COX6A1", "DYNLL1", "RSRC2", "UBC", "RAN", "MPHOSPH8", "SAP18", "RPL21", "POMP", "HMGB1", "HSPH1", "N4BP2L2", "ELF1", "TSC22D1", "TPT1", "ITM2B", "COMMD6", "ARGLU1", "HNRNPC", "DAD1", "NEDD8", "NFKBIA", "PNN", "RPS29", "RPL36AL", "LGALS3", "KTN1", "SYNE2", "ZFP36L1", "SRSF5", "RBM25", "NPC2", "TMED10", "FOS", "CALM1", "DDX24", "IFI27", "HSP90AA1", "EIF5", "ATP5MPL", "SRP14", "PDIA3", "SERF2", "B2M", "EID1", "ANXA2", "TPM1", "RPS27L", "PPIB", "RPL4", "RPLP1", "PKM", "MORF4L1", "SEC11A", "AKAP13", "CIB1", "IQGAP1", "SELENOS", "RPS2", "SRRM2", "ELOB", "LITAF", "RPS15A", "FUS", "MT2A", "COX4I1", "MAP1LC3B", "CYBA", "APRT", "ANKRD11", "RPL13", "TCF25", "YWHAE", "PFN1", "RPL26", "UBB", "WSB1", "RPL23A", "ZNF207", "RPL23", "RPL19", "IGFBP4", "KRT19", "EIF1", "STAT3", "RPL27", "LUC7L3", "TOB1", "SPAG9", "VMP1", "DDX5", "RPL38", "SUMO2", "H3F3B", "SRSF2", "SOCS3", "TIMP2", "RNF213", "ACTG1", "P4HB", "MYL12A", "MYL12B", "ANKRD12", "VAPA", "FKBP1A", "DSTN", "RRBP1", "CST3", "RBM39", "TOP1", "YWHAB", "ZFAS1", "CEBPB", "PMEPA1", "GNAS", "ATP5F1E", "PSMA7", "RPS21", "PPDPF", "GPX4", "ATP5F1D", "MIDN", "CIRBP", "RPS15", "OAZ1", "GADD45B", "EEF2", "RPL36", "RPS28", "UBL5", "JUNB", "CALR", "IER2", "DNAJB1", "TPM4", "KLF2", "RPL18A", "JUND", "UBA52", "FXYD5", "COX6B1", "SPINT2", "EIF3K", "ACTN4", "ZFP36", "RPS16", "CEACAM6", "RPS19", "RABAC1", "FOSB", "SNRPD2", "NOP53", "SELENOW", "RPL18", "PPP1R15A", "FTL", "RPL13A", "RPS11", "FCGRT", "MYADM", "RPS9", "RPL28", "RPS5", "UQCR10", "MYH9", "LGALS1", "DDX17", "RPL3", "ATF4", "ST13", "RBX1", "SNU13", "TSPO", "ATP5PF", "APP", "SOD1", "SON", "TTC3", "HMGN1", "CSTB", "PTTG1IP", "MT-ND1", "MT-ND2", "MT-CO1", "MT-CO2", "MT-ATP8", "MT-ATP6", "MT-CO3", "MT-ND3", "MT-ND4L", "MT-ND4", "MT-ND5", "MT-ND6", or "MT-CYB", not "counts". Run rlang::last_trace() to see where the error occurred.

sessionInfo() R version 4.2.2 (2022-10-31) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Red Hat Enterprise Linux 8.8 (Ootpa)

Matrix products: default BLAS/LAPACK: /nas/longleaf/rhel8/apps/r/4.2.2/lib/libopenblas_haswellp-r0.3.20.so

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

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

other attached packages: [1] Seurat_5.0.1 SeuratObject_5.0.0 sp_2.1-1

loaded via a namespace (and not attached): [1] Rtsne_0.16 colorspace_2.1-0 deldir_1.0-9 ellipsis_0.3.2 ggridges_0.5.4 RcppHNSW_0.5.0
[7] rstudioapi_0.15.0 spatstat.data_3.0-3 leiden_0.4.3.1 listenv_0.9.0 remotes_2.4.2.1 ggrepel_0.9.4
[13] RSpectra_0.16-1 fansi_1.0.5 codetools_0.2-19 splines_4.2.2 R.methodsS3_1.8.2 polyclip_1.10-6
[19] spam_2.10-0 jsonlite_1.8.7 ica_1.0-3 cluster_2.1.4 png_0.1-8 R.oo_1.25.0
[25] uwot_0.1.16 shiny_1.8.0 sctransform_0.4.1 spatstat.sparse_3.0-3 compiler_4.2.2 httr_1.4.7
[31] Matrix_1.6-3 fastmap_1.1.1 lazyeval_0.2.2 cli_3.6.1 later_1.3.1 prettyunits_1.2.0
[37] htmltools_0.5.7 tools_4.2.2 igraph_1.5.1 dotCall64_1.1-0 gtable_0.3.4 glue_1.6.2
[43] RANN_2.6.1 reshape2_1.4.4 dplyr_1.1.3 Rcpp_1.0.11 scattermore_1.2 vctrs_0.6.4
[49] spatstat.explore_3.2-5 nlme_3.1-163 progressr_0.14.0 lmtest_0.9-40 spatstat.random_3.2-1 stringr_1.5.1
[55] ps_1.7.5 globals_0.16.2 mime_0.12 miniUI_0.1.1.1 lifecycle_1.0.4 irlba_2.3.5.1
[61] goftest_1.2-3 future_1.33.0 MASS_7.3-60 zoo_1.8-12 scales_1.2.1 promises_1.2.1
[67] spatstat.utils_3.0-4 parallel_4.2.2 RColorBrewer_1.1-3 reticulate_1.34.0 pbapply_1.7-2 gridExtra_2.3
[73] ggplot2_3.4.4 stringi_1.8.1 fastDummies_1.7.3 pkgbuild_1.4.2 rlang_1.1.2 pkgconfig_2.0.3
[79] matrixStats_1.1.0 lattice_0.22-5 ROCR_1.0-11 purrr_1.0.2 tensor_1.5 patchwork_1.1.3
[85] htmlwidgets_1.6.2 processx_3.8.2 cowplot_1.1.1 tidyselect_1.2.0 parallelly_1.36.0 RcppAnnoy_0.0.21
[91] plyr_1.8.9 magrittr_2.0.3 R6_2.5.1 generics_0.1.3 pillar_1.9.0 fitdistrplus_1.1-11
[97] survival_3.5-7 abind_1.4-5 tibble_3.2.1 future.apply_1.11.0 crayon_1.5.2 KernSmooth_2.23-22
[103] utf8_1.2.4 spatstat.geom_3.2-7 plotly_4.10.3 grid_4.2.2 data.table_1.14.8 callr_3.7.3
[109] digest_0.6.33 xtable_1.8-4 tidyr_1.3.0 httpuv_1.6.12 R.utils_2.12.2 munsell_0.5.0
[115] viridisLite_0.4.2

sc[["percent_MT"]] <- PercentageFeatureSet(sc, pattern = "^MT-|^mt-")

[wangchuanyuan1]

Me too, this only seems to happen in the latest version (V5.0.0)

[menage95]

I am also having this issue after updating packages - did you find a resolution?

[menage95]

UPDATE: after installing the development version of Signac to solve another bug, this issue also didn't happen again

[mhkowalski]

Hi, I am not able to reproduce this with the latest versions of Seurat (5.0.1) and SeuratObject (5.0.1). Could you please try upgrading and let me know if the issue persists/ provide a reproducible example?

[hyhy200g]

I have the same issue at the latest versions of Seurat (5.0.1) and SeuratObject (5.0.1)

[klgoss]

Did anyone find a resolution to this? I'm having the same issue with code that used to work and now getting this error since updating to V5.

[victorjima]

Hello, I have been experiencing this issue for two days and I finally sorted it out by updating Signac to github version (I also updated SeuratData and others). Hope it works for you!

[Nglab]

So same thing happened to me (installing scCustomize might have been the culprit but I am not 100% certain). I have tried reinstalling Seurat and Signac but it didn't work for me. The way I fixed this without digging deep into the code or finding out which package(s) needs updating/re-updating was clearing out my user libPath and rebuilt all the packages (for me, it was just Seurat, Signac, and EnsDb.Hsapiens.v86) from scratch.

[Clara22]

In case you don't want to update to the Signac github version, providing the features / gene names instead of a pattern to PercentageFeatureSet worked for me:

#Create a vector with the gene names you want to work with, in this case any gene name in the 'counts' slot starting with 'mt-'
selgenes<-rownames(SEU@assays$RNA@counts)[grepl(pattern="^mt-",rownames(SEU@assays$RNA@counts))]

The selgenes vector looks like this (I am working with a mouse dataset, hence the lowercase)

selgenes [1] "mt-Nd1" "mt-Nd2" "mt-Co1" "mt-Co2" "mt-Atp8" "mt-Atp6" "mt-Co3" [8] "mt-Nd3" "mt-Nd4l" "mt-Nd4" "mt-Nd5" "mt-Nd6" "mt-Cytb"

#Run PercentageFeatureSet giving the vector of gene names to features
SEU <- PercentageFeatureSet(SEU, features=selgenes, assay="RNA", col.name="percent.mt")

[zm2647]

@Clara22 I followed your code above,but there was an error like this

selgenes<-rownames(seurat_merge@assays$RNA@counts)[grepl(pattern="^MT-",rownames(seurat_merge@assays$RNA@counts))] seurat_merge[["percent.mt"]] <- PercentageFeatureSet(seurat_merge, assay="RNA", features=selgenes, col.name="percent.mt") Error in [<-.data.frame(*tmp*, , i, value = new("Seurat", assays = list( : There are 58715 rows in the replacement data, but the data is 33145 do you know what the problem is?

[zm2647]

and I found 58715 is the rowcount of seurat_merge@assays$RNA, 33145 is the colcount

[igrabski]

Closing this issue since it seems that re-installing to the versions provided above resolves the problem -- please feel free to open a new issue if problems persist.