Error coercing GeoMx data to Seurat object

[generalshermanw]

Dear team,

I'm attempting to do a conversion between NanoStringGeoMxSet to a Seurat object using the GeoMxTools::as.Seurat() function. The relevant error is:
Error in names(v) <- row.names(x = value) : 'names' attribute [179] must be the same length as the vector [1]
Command:
seuratData <- as.Seurat(targetData, assay = NULL, normData = 'q_norm', coordinates = NULL, forceRaw = FALSE)
I think I've worked through enough that I believe the issue stems from the Seurat::AddMetaData command. However, I've hit a dead end on the debug at this point.

Would greatly appreciate your support. Thanks!

Relevant environment:

R version 4.2.2 (2022-10-31)
Platform: x86_64-pc-linux-gnu (64-bit)
other attached packages:
[1] Seurat_4.9.9.9058 SeuratObject_5.0.0 sp_2.1-1 GeomxTools_3.2.0 NanoStringNCTools_1.6.1
[6] ggplot2_3.4.4 S4Vectors_0.36.2 Biobase_2.58.0 BiocGenerics_0.44.0

[maddygriz]

Hi @generalshermanw,

Our customer support team will be able to help you with this. Please email support@nanostring.com with your issue.

Thanks,
Maddy

[zchatt]

Hi all.,

Was there a solution for this? I am having the exact same issue using the same GeoMxSet object that was working ~2 months ago.

`R version 4.3.1 (2023-06-16)
Platform: aarch64-apple-darwin20 (64-bit)
Running under: macOS Ventura 13.6.1

Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libRlapack.dylib; LAPACK version 3.11.0

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: Australia/Sydney
tzcode source: internal

attached base packages:
[1] stats4 stats graphics grDevices utils datasets methods base

other attached packages:
[1] terra_1.7-55 harmony_1.1.0 Rcpp_1.0.11 ggpubr_0.6.0 SeuratObject_5.0.0
[6] Seurat_4.4.0 preprocessCore_1.62.1 GiottoClass_0.0.0.9005 GiottoUtils_0.0.0.9003 Giotto_3.3.1
[11] devtools_2.4.5 usethis_2.2.2 GeomxTools_3.3.0 NanoStringNCTools_1.8.0 ggplot2_3.4.4
[16] S4Vectors_0.38.2 Biobase_2.60.0 BiocGenerics_0.46.0 `

[maddygriz]

Hi @zchatt,

Our customer support team will be able to help you with this. Please email support@nanostring.com with your issue.

Thanks,
Maddy

[dksenthil]

I got into a similar error , which I could reproduce for the demoData
I think as.Seurat function n Seurat5 is no longer accepting GeoMx dataset. This could be a Seurat issue.

demoSeurat <- as.Seurat(norm_target_demoData, normData = "q_norm")
Error in validObject(object = object) : 
  invalid class “Seurat” object: 'project' cannot be an empty character 

[maddygriz]

Hi @dksenthil,

GeomxTools does not support Seurat v5 coercion yet. Please revert to Seurat v4.4 to coerce a GeoMxSet object to Seurat. We are working to get Seurat v5 coercion available in our next release.

Thanks,
Maddy

[dksenthil]

Thanks, Meanwhile if there is anyone looking for a quick workaround.
Not the best way, but it still works!

# create v3 assays
options(Seurat.object.assay.version = "v3")
target_demoData_SPE <- as.SpatialExperiment(target_demoData, normData = "q_norm")
counts <- SummarizedExperiment::assay(target_demoData_SPE)
meta <- SummarizedExperiment::colData(target_demoData_SPE) %>%as.data.frame
target_demoData_seurat <- CreateSeuratObject(counts = counts,project = "SPE_toSeurat",  meta.data = meta, assay = "GeoMx")

~