issue with running paramsweep

[el-hodiri]

Hello!

I am trying to run DoubletFinder on a Seurat object merged from 8 individual objects. The merged object is called HK_merged and the individual org=iginal objects have names like ControlA, ControlB, etc

'''R

sweep.res.list_HK <- paramSweep(HK_merge, PCs = 1:20, sct = FALSE)
Error in .subscript.2ary(x, , j, drop = TRUE) : subscript out of bounds
In addition: Warning message:
In LayerData.Assay5(object = x, layer = i) :
multiple layers are identified by counts.ControlA counts.ControlB counts.ControlC counts.CancerA counts.CancerB counts.CancerC counts.InjuryA counts.InjuryB
only the first layer is used
'''

Would you please help me figure out what I'm doing wrong?

Thanks in advance!

Here is my session info:

'''

sessionInfo()
R version 4.4.1 (2024-06-14)
Platform: x86_64-apple-darwin20
Running under: macOS Sonoma 14.6.1

Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/lib/libRlapack.dylib; LAPACK version 3.12.0

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

time zone: America/New_York
tzcode source: internal

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

other attached packages:
[1] fields_16.3 viridisLite_0.4.2 spam_2.10-0 DoubletFinder_2.0.4 dplyr_1.1.4 Seurat_5.1.0
[7] SeuratObject_5.0.2 sp_2.1-4

loaded via a namespace (and not attached):
[1] deldir_2.0-4 pbapply_1.7-2 gridExtra_2.3 rlang_1.1.4 magrittr_2.0.3
[6] RcppAnnoy_0.0.22 matrixStats_1.3.0 ggridges_0.5.6 compiler_4.4.1 spatstat.geom_3.3-2
[11] maps_3.4.2 png_0.1-8 vctrs_0.6.5 reshape2_1.4.4 stringr_1.5.1
[16] pkgconfig_2.0.3 fastmap_1.2.0 utf8_1.2.4 promises_1.3.0 purrr_1.0.2
[21] jsonlite_1.8.8 goftest_1.2-3 later_1.3.2 spatstat.utils_3.0-5 irlba_2.3.5.1
[26] cluster_2.1.6 R6_2.5.1 ica_1.0-3 stringi_1.8.4 RColorBrewer_1.1-3
[31] spatstat.data_3.1-2 reticulate_1.38.0 parallelly_1.38.0 spatstat.univar_3.0-0 lmtest_0.9-40
[36] scattermore_1.2 Rcpp_1.0.13 tensor_1.5 future.apply_1.11.2 zoo_1.8-12
[41] sctransform_0.4.1 httpuv_1.6.15 Matrix_1.7-0 splines_4.4.1 igraph_2.0.3
[46] tidyselect_1.2.1 rstudioapi_0.16.0 abind_1.4-5 spatstat.random_3.3-1 codetools_0.2-20
[51] miniUI_0.1.1.1 spatstat.explore_3.3-1 listenv_0.9.1 lattice_0.22-6 tibble_3.2.1
[56] plyr_1.8.9 shiny_1.9.1 ROCR_1.0-11 Rtsne_0.17 future_1.34.0
[61] fastDummies_1.7.3 survival_3.7-0 polyclip_1.10-7 fitdistrplus_1.2-1 pillar_1.9.0
[66] KernSmooth_2.23-24 plotly_4.10.4 generics_0.1.3 RcppHNSW_0.6.0 ggplot2_3.5.1
[71] munsell_0.5.1 scales_1.3.0 globals_0.16.3 xtable_1.8-4 glue_1.7.0
[76] lazyeval_0.2.2 tools_4.4.1 data.table_1.15.4 RSpectra_0.16-2 RANN_2.6.1
[81] leiden_0.4.3.1 dotCall64_1.1-1 cowplot_1.1.3 grid_4.4.1 tidyr_1.3.1
[86] colorspace_2.1-1 nlme_3.1-165 patchwork_1.2.0 cli_3.6.3 spatstat.sparse_3.1-0
[91] fansi_1.0.6 uwot_0.2.2 gtable_0.3.5 digest_0.6.37 progressr_0.14.0
[96] ggrepel_0.9.5 htmlwidgets_1.6.4 htmltools_0.5.8.1 lifecycle_1.0.4 httr_1.4.7
[101] mime_0.12 MASS_7.3-61

'''

[EDePasquale]

I haven't gotten this error with DoubletFinder, but with another tool, and I fixed it by joining my layers. Have you used the JoinLayers yet to see if that fixes it?

[floresans]

Hi , you should use DoubletFinder before merging the data. Apply paramSweep separately or as a for loop to find pK. then, you can merge.