Closed SarahMyoblast closed 1 year ago
jarchana09
commented
1 year ago Hi, Not sure if this helps, but you could try including quotes around the identities E115_2 and E95_2 and running FindMarkers.
early.stage.differential.markers <- FindMarkers(somite_2.combined, ident.1 = "E115_2", ident.2 = "E95_2", verbose = FALSE)
Thanks.
saketkc
commented
1 year ago If you are using the lognorm workflow you should switch to RNA assay before running find markers:
b.interferon.response <- FindMarkers(immune.combined, ident.1 = "E115_2", ident.2 = "E95_2", verbose = FALSE, assay="RNA")If you are using SCT workflow, you should do:
b.interferon.response <- FindMarkers(immune.combined, ident.1 = "E115_2", ident.2 = "E95_2", verbose = FALSE, assay="SCT")DE should not be run on the integrated assay (which is the default assay post running the integration workflow).
Hi,
I encountered an error when following the vignette "introduction to scRNA-seq integration".
When I run the line
b.interferon.response <- [FindMarkers](https://satijalab.org/seurat/reference/FindMarkers.html)(immune.combined, ident.1 = "B_STIM", ident.2 = "B_CTRL", verbose = FALSE)Modified for my data: `early.stage.differential.markers <- FindMarkers(somite_2.combined, ident.1 = E115_2, ident.2 = E95_2, verbose = FALSE)
`I get this error:
Matrix products: default LAPACK: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRlapack.dylib
locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages: [1] stats4 parallel stats graphics grDevices utils datasets methods base
other attached packages: [1] ggplot2_3.4.0 cowplot_1.1.1 patchwork_1.1.2 SeuratObject_4.0.4
[5] Seurat_4.1.0 dplyr_1.0.10 monocle3_0.2.3.0 SingleCellExperiment_1.12.0 [9] SummarizedExperiment_1.20.0 GenomicRanges_1.42.0 GenomeInfoDb_1.26.7 IRanges_2.24.1
[13] S4Vectors_0.28.1 MatrixGenerics_1.2.1 matrixStats_0.63.0 Biobase_2.50.0
[17] BiocGenerics_0.36.1
loaded via a namespace (and not attached): [1] Rtsne_0.16 colorspace_2.0-3 deldir_1.0-6 ellipsis_0.3.2 ggridges_0.5.4
[6] XVector_0.30.0 rstudioapi_0.14 spatstat.data_3.0-0 farver_2.1.1 leiden_0.4.3
[11] listenv_0.9.0 ggrepel_0.9.2 fansi_1.0.3 codetools_0.2-18 splines_4.0.4
[16] polyclip_1.10-4 jsonlite_1.8.4 ica_1.0-3 cluster_2.1.4 png_0.1-8
[21] uwot_0.1.14 shiny_1.7.4 sctransform_0.3.5 spatstat.sparse_3.0-0 BiocManager_1.30.19
[26] compiler_4.0.4 httr_1.4.4 assertthat_0.2.1 Matrix_1.5-3 fastmap_1.1.0
[31] lazyeval_0.2.2 cli_3.5.0 later_1.3.0 htmltools_0.5.4 tools_4.0.4
[36] igraph_1.3.5 gtable_0.3.1 glue_1.6.2 GenomeInfoDbData_1.2.4 RANN_2.6.1
[41] reshape2_1.4.4 tinytex_0.43 Rcpp_1.0.9 scattermore_0.8 vctrs_0.5.1
[46] nlme_3.1-161 lmtest_0.9-40 xfun_0.36 stringr_1.5.0 globals_0.16.2
[51] mime_0.12 miniUI_0.1.1.1 lifecycle_1.0.3 irlba_2.3.5.1 goftest_1.2-3
[56] future_1.30.0 zlibbioc_1.36.0 MASS_7.3-58.1 zoo_1.8-11 scales_1.2.1
[61] spatstat.core_2.2-0 promises_1.2.0.1 spatstat.utils_3.0-1 RColorBrewer_1.1-3 reticulate_1.20
[66] pbapply_1.6-0 gridExtra_2.3 rpart_4.1.19 stringi_1.7.8 rlang_1.0.6
[71] pkgconfig_2.0.3 bitops_1.0-7 lattice_0.20-45 ROCR_1.0-11 purrr_1.0.0
[76] tensor_1.5 labeling_0.4.2 htmlwidgets_1.6.0 tidyselect_1.2.0 parallelly_1.33.0
[81] RcppAnnoy_0.0.20 plyr_1.8.8 magrittr_2.0.3 R6_2.5.1 generics_0.1.3
[86] DelayedArray_0.16.3 DBI_1.1.3 withr_2.5.0 pillar_1.8.1 mgcv_1.8-41
[91] fitdistrplus_1.1-8 survival_3.4-0 abind_1.4-5 RCurl_1.98-1.9 tibble_3.1.8
[96] future.apply_1.10.0 KernSmooth_2.23-20 utf8_1.2.2 spatstat.geom_3.0-3 plotly_4.10.1
[101] viridis_0.6.2 grid_4.0.4 data.table_1.14.6 digest_0.6.31 xtable_1.8-4
[106] tidyr_1.2.1 httpuv_1.6.7 munsell_0.5.0 viridisLite_0.4.1