FoldChange vs FindMarkers give differnet log fc results

[coralzhang]

I encountered a similar issue reported here https://www.biostars.org/p/9478554/
Here is an example,
mat1=FoldChange(pbmc_small, ident.1 = 1); mat2 <- FindMarkers(object = pbmc_small, ident.1 = 1); mat1["MS4A1",]; mat2["MS4A1",];
This is the output:

mat1["MS4A1",]
avg_log2FC pct.1 pct.2
MS4A1 -0.6837357 0.08 0.182

mat2["MS4A1",]
p_val avg_log2FC pct.1 pct.2 p_val_adj
MS4A1 0.1840551 -4.289191 0.08 0.182 1

[longmanz]

Hi,
Can you try the latest version of Seurat? This logfc issue should be fixed now.

[coralzhang]

Thank you for your response. But I tried to reinstall using this
install_github("satijalab/seurat")
Then tried this
`> library(Seurat)

mat1=FoldChange(pbmc_small, ident.1 = 1); mat2 <- FindMarkers(object = pbmc_small, ident.1 = 1); mat1["MS4A1",]; mat2["MS4A1",];
|++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s
avg_log2FC pct.1 pct.2
MS4A1 -0.6837357 0.08 0.182
p_val avg_log2FC pct.1 pct.2 p_val_adj
MS4A1 0.1840551 -4.289191 0.08 0.182 1`

Here is the sessioninfo

sessionInfo()
R version 4.2.1 (2022-06-23)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Big Sur ... 10.16

Matrix products: default
BLAS: /Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libRblas.0.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.2/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] stats graphics grDevices utils datasets methods base

other attached packages:
[1] devtools_2.4.5 usethis_2.1.6 SeuratObject_4.1.3 Seurat_4.3.0

[lucygarner]

Hi,

I am having the same issue with Seurat 4.3.0. The FoldChange and FindMarkers functions give me very different fold change values. The DefaultAssay of my Seurat object is "RNA".

markers <- FindMarkers(seurat_obj, ident.1 = "TCR", ident.2 = "unstim")
fold_change <- FoldChange(seurat_obj, ident.1 = "TCR", ident.2 = "unstim")

markers["CCL4", ]
p_val avg_log2FC pct.1 pct.2 p_val_adj
CCL4 0 5.550652 0.962 0.685 0

fold_change["CCL4", ]
avg_log2FC pct.1 pct.2
CCL4 1.264632 0.962 0.685

Your advice or explanation would be much appreciated. Which are the "correct" fold change values? I would like to obtain fold change values for all genes.

Best wishes,
Lucy

sessionInfo()

R version 4.2.0 (2022-04-22)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)

Matrix products: default
BLAS: /Filers/package/R-base/4.2.0/lib64/R/lib/libRblas.so
LAPACK: /Filers/package/R-base/4.2.0/lib64/R/lib/libRlapack.so

locale:
[1] LC_CTYPE=en_GB.UTF-8 LC_NUMERIC=C LC_TIME=en_GB.UTF-8
[4] LC_COLLATE=en_GB.UTF-8 LC_MONETARY=en_GB.UTF-8 LC_MESSAGES=en_GB.UTF-8
[7] LC_PAPER=en_GB.UTF-8 LC_NAME=C LC_ADDRESS=C
[10] LC_TELEPHONE=C LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C

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

other attached packages:
[1] forcats_1.0.0 stringr_1.5.0 dplyr_1.1.0 purrr_1.0.1
[5] readr_2.1.3 tidyr_1.3.0 tibble_3.1.8 ggplot2_3.4.0
[9] tidyverse_1.3.2 SeuratObject_4.1.3 Seurat_4.3.0

loaded via a namespace (and not attached):
[1] googledrive_2.0.0 Rtsne_0.16 colorspace_2.1-0
[4] deldir_1.0-6 ellipsis_0.3.2 ggridges_0.5.4
[7] fs_1.6.0 rstudioapi_0.14 spatstat.data_3.0-0
[10] leiden_0.4.3 listenv_0.9.0 ggrepel_0.9.2
[13] lubridate_1.9.1 fansi_1.0.4 xml2_1.3.3
[16] codetools_0.2-19 splines_4.2.0 knitr_1.42
[19] polyclip_1.10-4 jsonlite_1.8.4 broom_1.0.3
[22] ica_1.0-3 dbplyr_2.3.0 cluster_2.1.4
[25] png_0.1-8 uwot_0.1.14 shiny_1.7.4
[28] sctransform_0.3.5 spatstat.sparse_3.0-0 compiler_4.2.0
[31] httr_1.4.4 backports_1.4.1 assertthat_0.2.1
[34] Matrix_1.5-3 fastmap_1.1.0 lazyeval_0.2.2
[37] gargle_1.3.0 cli_3.6.0 later_1.3.0
[40] htmltools_0.5.4 tools_4.2.0 igraph_1.3.5
[43] gtable_0.3.1 glue_1.6.2 RANN_2.6.1
[46] reshape2_1.4.4 Rcpp_1.0.10 scattermore_0.8
[49] cellranger_1.1.0 vctrs_0.5.2 spatstat.explore_3.0-5
[52] nlme_3.1-162 progressr_0.13.0 lmtest_0.9-40
[55] spatstat.random_3.0-1 xfun_0.37 globals_0.16.2
[58] rvest_1.0.3 timechange_0.2.0 mime_0.12
[61] miniUI_0.1.1.1 lifecycle_1.0.3 irlba_2.3.5.1
[64] googlesheets4_1.0.1 goftest_1.2-3 future_1.31.0
[67] MASS_7.3-58.2 zoo_1.8-11 scales_1.2.1
[70] hms_1.1.2 promises_1.2.0.1 spatstat.utils_3.0-1
[73] parallel_4.2.0 RColorBrewer_1.1-3 yaml_2.3.7
[76] reticulate_1.28 pbapply_1.7-0 gridExtra_2.3
[79] stringi_1.7.12 rlang_1.0.6 pkgconfig_2.0.3
[82] matrixStats_0.63.0 evaluate_0.20 lattice_0.20-45
[85] ROCR_1.0-11 tensor_1.5 patchwork_1.1.2
[88] htmlwidgets_1.6.1 cowplot_1.1.1 tidyselect_1.2.0
[91] parallelly_1.34.0 RcppAnnoy_0.0.20 plyr_1.8.8
[94] magrittr_2.0.3 R6_2.5.1 generics_0.1.3
[97] DBI_1.1.3 withr_2.5.0 haven_2.5.1
[100] pillar_1.8.1 fitdistrplus_1.1-8 survival_3.5-0
[103] abind_1.4-5 sp_1.6-0 future.apply_1.10.0
[106] crayon_1.5.2 modelr_0.1.10 KernSmooth_2.23-20
[109] utf8_1.2.3 spatstat.geom_3.0-6 plotly_4.10.1
[112] tzdb_0.3.0 rmarkdown_2.20 readxl_1.4.1
[115] grid_4.2.0 data.table_1.14.6 reprex_2.0.2
[118] digest_0.6.31 xtable_1.8-4 httpuv_1.6.8
[121] munsell_0.5.0 viridisLite_0.4.1

[saketkc]

Apologies everyone for the delay.

I have just pushed 992c1a9 to develop branch which should fix this and related issues. Can you pull from the develop branch and re-open this issue if you are still facing issues?

devtools::install_github("satijalab/seurat", ref="develop")