Comments (15)
browaeysrobin
commented on September 26, 2024
1
Hi @jaquol
Deleting the SCT and integrated assays is only a temporary solution to this error of course.
I tried to reproduce the error, but again, everything runs fine with me and I can select different assays (RNA, SCT) via the get_expressed_genes function. In my case Assays(seurat_obj) returns a vector and not a list, in contrast to what you mentioned before. Maybe there is again an issue with a conflict with another package (as for your other issue)?
The selection of which slot (RNA/SCT/integrated) in this get_expressed_genes() function will only effect which genes will be considered to be expressed (which affects the background of genes for the ligand activity analysis and the selection of ligands/receptors used as input for this). This warning that this function throws when having a SCT and/or integrated assay in addition to the RNA assay is just to let users think about whether the way get_expressed_genes() defines expressed genes is a correct way to do it for transformed data. get_expressed_genes() will look at the fraction of cells having a non-zero expression value for a specific gene. Because data transformation could change zeroes to non-zeroes and vice versa, I would recommend using the unaffected RNA slot. But, out of experience I can say that choosing SCT / RNA / integrated does not make much difference in which genes you get out as expressed in the end. Typically, choosing RNA will result in a slightly higher number of expressed genes, but differences in number are minor (eg 5950 vs 6000 expressed genes).
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browaeysrobin
commented on September 26, 2024
Hi @jaquol,
I would suggest setting assay_oi = 'RNA' to define expressed genes. Can you check whether this works?
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jaquol
commented on September 26, 2024
Hi @browaeysrobin,
Thank you for your quick reply! I am afraid that assay_oi = 'RNA' does not work either on my side; I get the same error as in my previous message.
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jaquol
commented on September 26, 2024
Hi @browaeysrobin,
I thought that I might be able to overcome the issue above by deleting the "SCT" and/or "integrated" assays. Inspired by this, I deleted both the "SCT" and "integrated" assays with:
seuratObj@assays$integrated <- NULL
seuratObj@assays$SCT <- NULL
Unlike previously, this way I do not get any warning when running the get_expressed_genes function:
expressed_genes_receiver = get_expressed_genes(receiver, seuratObj, pct = 0.10)
My questions are then:
- Does deleting the "SCT" and "integrated" assays makes sense?
- Is "RNA" the preferred assay to run nichenetr on?
Thank you!
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tkapello
commented on September 26, 2024
I started implementing the NicheNet code to my sc dataset and I wanted to report the same issue. Switching the argument to "RNA" does not work:
>expressed_genes_receiver = get_expressed_genes(receiver, baldataset, pct = 0.10, assay_oi = 'RNA')
Error in .normarg_assays(assays) :
'assays' must be a SimpleList, list or array
In my case, the integrated gene list is a lot smaller so I d rather use the RNA assay to have a bigger expressed gene list. If deleting the integrated slot works for some people, I would do it, but of course, an alternative would be more preferable.
Thanks in advance,
Theo
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browaeysrobin
commented on September 26, 2024
Hi @tkapello
Is it possible you loaded the SummarizedExperiment package? If yes, could you try to run this code again without loading SummarizedExperiment?
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tkapello
commented on September 26, 2024
SummarizedExperiment seems to be needed, otherwise:
Error in Assays(seurat_obj) : could not find function "Assays"
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browaeysrobin
commented on September 26, 2024
Hi @tkapello
Normally, SummarizedExperiment is not needed, because Assays() is also function of the Seurat package. So: did you load the Seurat package (should be yes)?
I also was able to replicate the error you both mentioned here above if SummarizedExperiment was loaded after loading nichenetr/Seurat/tidyverse (because it overwrites some functions of Seurat/base R/tidyverse and loads other packages that also overwrite functions of Seurat/base R/tidyverse). However, no error was thrown when SummarizedExperiment was loaded before.
So: I don't think there is an issue if you do the following
library(nichenetr)
library(Seurat)
library(tidyverse)
seurat_obj = readRDS("data/seuratObj.rds")
expressed_genes_receiver = get_expressed_genes("celltype X", seurat_obj, pct = 0.10)
Here, Assays should be used from Seurat.
If you do want to load other packages, the following should work:
library(SummarizedExperiments) # and other packages if really necessary
library(nichenetr)
library(Seurat)
library(tidyverse)
seurat_obj = readRDS("data/seuratObj.rds")
expressed_genes_receiver = get_expressed_genes("celltype X", seurat_obj, pct = 0.10)
In the near future, I will change the underlying code to avoid these conflicts such that the order in which you load the packages should not matter.
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tkapello
commented on September 26, 2024
I tried the order of the packages you suggested, but the error remains:
Error in .normarg_assays(assays) :
'assays' must be a SimpleList, list or array
Does the Seurat object need to be loaded as a .rds? I load a class Seurat object from my environment.
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browaeysrobin
commented on September 26, 2024
Hi @tkapello
Could you once try this to see whether this resolves the issue?
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tkapello
commented on September 26, 2024
I tried everything you suggested and still I get the same error :-(
Error in .normarg_assays(assays) :
'assays' must be a SimpleList, list or array
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browaeysrobin
commented on September 26, 2024
Hi @tkapello
Could you try to
- re-install nichenetr and run your script again ?
- let me know whether it works now and if not: provide me with your
sessionInfo()?
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tkapello
commented on September 26, 2024
I uninstalled and re-installed nichenetr and now I have the following error:
> # Define a receiver cell type
> receiver = "Neutrophil_0"
> expressed_genes_receiver = get_expressed_genes(receiver, baldataset, pct = 0.10, assay_oi = 'RNA')
Error: 'Assays' is not an exported object from 'namespace:Seurat'
As you requested, my SessionInfo():
> sessionInfo()
R version 3.5.3 (2019-03-11)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Debian GNU/Linux 9 (stretch)
Matrix products: default
BLAS: /usr/lib/openblas-base/libblas.so.3
LAPACK: /usr/lib/libopenblasp-r0.2.19.so
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8
[4] LC_COLLATE=en_US.UTF-8 LC_MONETARY=en_US.UTF-8 LC_MESSAGES=C
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C LC_ADDRESS=C
[10] LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] parallel stats4 stats graphics grDevices utils datasets methods base
other attached packages:
[1] circlize_0.4.6 forcats_0.4.0 stringr_1.4.0
[4] dplyr_0.8.0.1 purrr_0.3.2 readr_1.3.1
[7] tidyr_0.8.3 tibble_2.1.1 ggplot2_3.1.0
[10] tidyverse_1.2.1 Seurat_3.0.0 nichenetr_0.1.0
[13] SummarizedExperiment_1.12.0 DelayedArray_0.8.0 BiocParallel_1.16.6
[16] matrixStats_0.54.0 Biobase_2.42.0 GenomicRanges_1.34.0
[19] GenomeInfoDb_1.18.2 IRanges_2.16.0 S4Vectors_0.20.1
[22] BiocGenerics_0.28.0 BiocManager_1.30.4
loaded via a namespace (and not attached):
[1] reticulate_1.12 R.utils_2.8.0 tidyselect_0.2.5 RSQLite_2.1.1
[5] AnnotationDbi_1.44.0 htmlwidgets_1.3 grid_3.5.3 Rtsne_0.15
[9] munsell_0.5.0 codetools_0.2-16 ica_1.0-2 future_1.12.0
[13] withr_2.1.2 GOSemSim_2.8.0 colorspace_1.4-1 rgexf_0.15.3
[17] knitr_1.22 rstudioapi_0.10 ROCR_1.0-7 DOSE_3.8.2
[21] gbRd_0.4-11 listenv_0.7.0 Rdpack_0.11-0 GenomeInfoDbData_1.2.0
[25] bit64_0.9-7 downloader_0.4 generics_0.0.2 ipred_0.9-8
[29] xfun_0.6 randomForest_4.6-14 R6_2.4.0 rsvd_1.0.0
[33] fgsea_1.8.0 bitops_1.0-6 assertthat_0.2.1 SDMTools_1.1-221
[37] scales_1.0.0 nnet_7.3-12 gtable_0.3.0 npsurv_0.4-0
[41] globals_0.12.4 timeDate_3043.102 rlang_0.3.3 GlobalOptions_0.1.0
[45] splines_3.5.3 lazyeval_0.2.2 ModelMetrics_1.2.2 acepack_1.4.1
[49] broom_0.5.1 brew_1.0-6 checkmate_1.9.1 yaml_2.2.0
[53] reshape2_1.4.3 modelr_0.1.4 backports_1.1.3 qvalue_2.14.1
[57] Hmisc_4.2-0 caret_6.0-82 DiagrammeR_1.0.0 tools_3.5.3
[61] lava_1.6.5 influenceR_0.1.0 gplots_3.0.1.1 RColorBrewer_1.1-2
[65] ggridges_0.5.1 Rcpp_1.0.1 plyr_1.8.4 base64enc_0.1-3
[69] visNetwork_2.0.6 zlibbioc_1.28.0 RCurl_1.95-4.12 rpart_4.1-13
[73] pbapply_1.4-0 viridis_0.5.1 cowplot_0.9.4 zoo_1.8-5
[77] haven_2.1.0 ggrepel_0.8.0 cluster_2.0.7-1 magrittr_1.5
[81] data.table_1.12.0 DO.db_2.9 lmtest_0.9-36 RANN_2.6.1
[85] fitdistrplus_1.0-14 hms_0.4.2 lsei_1.2-0 XML_3.98-1.19
[89] readxl_1.3.1 gridExtra_2.3 shape_1.4.4 compiler_3.5.3
[93] KernSmooth_2.23-15 crayon_1.3.4 R.oo_1.22.0 htmltools_0.3.6
[97] Formula_1.2-3 lubridate_1.7.4 DBI_1.0.0 MASS_7.3-51.3
[101] Matrix_1.2-17 cli_1.1.0 R.methodsS3_1.7.1 gdata_2.18.0
[105] metap_1.1 gower_0.2.0 igraph_1.2.4 pkgconfig_2.0.2
[109] foreign_0.8-71 plotly_4.9.0 recipes_0.1.5 xml2_1.2.0
[113] foreach_1.4.4 XVector_0.22.0 prodlim_2018.04.18 bibtex_0.4.2
[117] rvest_0.3.2 digest_0.6.18 sctransform_0.2.0 tsne_0.1-3
[121] fastmatch_1.1-0 cellranger_1.1.0 htmlTable_1.13.1 Rook_1.1-1
[125] gtools_3.8.1 nlme_3.1-137 jsonlite_1.6 viridisLite_0.3.0
[129] limma_3.38.3 pillar_1.3.1 lattice_0.20-38 GO.db_3.6.0
[133] httr_1.4.0 survival_2.44-1.1 glue_1.3.1 fdrtool_1.2.15
[137] png_0.1-7 iterators_1.0.10 bit_1.1-14 class_7.3-15
[141] stringi_1.4.3 blob_1.1.1 memoise_1.1.0 latticeExtra_0.6-28
[145] caTools_1.17.1.2 irlba_2.3.3 future.apply_1.2.0 ape_5.3
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browaeysrobin
commented on September 26, 2024
Hi @tkapello
It seems that your Seurat version is not the most recent. Could you try to reinstall the newest version?
Can you then first try to run Seurat::Assays() on your seurat object, and then run get_expressed_genes() from nichenetr again? And let me know which of these tests did work (and which not).
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tkapello
commented on September 26, 2024
you were right, it was the Seurat version. There was no Assays function
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Related Issues (20)
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