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Nanostring-Biostats / GeomxTools

Tools for NanoString GeoMx Digital Spatial Profiler data for reading DCC and PKC files to NanoStringGeomxSet class, Normalization and QC.
MIT License
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error using as.Seurat #176

Closed yupingz closed 1 year ago

yupingz commented 2 years ago

Hi,

Thank you for making this tool. I have problem using the Coercion of GeoMxSet to Seurat function. I could not figure out why as.Seurat didn't work for me. I was running the testing code. Any insight what was wrong?

library(GeomxTools) datadir <- system.file("extdata", "DSP_NGS_Example_Data", package = "GeomxTools") demoData <- readRDS(file.path(datadir, "/demoData.rds")) target_demoData <- aggregateCounts(demoData[1:1000,1:10]) Warning message: In aggregateCounts(demoData[1:1000, 1:10]) : Object has no negatives. No summary statistics for negatives will be calculated. target_demoData <- normalize(target_demoData, "quant") seurat_demoData <- as.Seurat(target_demoData, ident = "cell_line", normData = "exprs_norm", forceRaw = FALSE) Error in UseMethod(generic = "as.Seurat", object = x) : no applicable method for 'as.Seurat' applied to an object of class "c('NanoStringGeoMxSet', 'NanoStringRccSet', 'ExpressionSet', 'eSet', 'VersionedBiobase', 'Versioned')" packageVersion("GeomxTools") [1] ‘3.0.1’

NicoleEO commented 2 years ago

Hi @yupingz,

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

Thanks, Nicole

LuShuYangMing commented 1 year ago

Also got the error information from as.Seurat function: ` DSP <- GeomxTools::as.Seurat(sce,normData = "q_norm")

Registered S3 methods overwritten by 'Seurat': method from
$.JackStrawData SeuratObject $.Seurat SeuratObject $.SeuratCommand SeuratObject $<-.Seurat SeuratObject [.Assay SeuratObject [.DimReduc SeuratObject [.Seurat SeuratObject [.SeuratCommand SeuratObject [[.Assay SeuratObject [[.DimReduc SeuratObject [[.Seurat SeuratObject levels<-.Seurat SeuratObject .DollarNames.JackStrawData SeuratObject .DollarNames.Seurat SeuratObject .DollarNames.SeuratCommand SeuratObject as.list.SeuratCommand SeuratObject as.logical.JackStrawData SeuratObject dim.Assay SeuratObject dim.DimReduc SeuratObject dim.Seurat SeuratObject dimnames.Assay SeuratObject dimnames.DimReduc SeuratObject dimnames.Seurat SeuratObject droplevels.Seurat SeuratObject length.DimReduc SeuratObject levels.Seurat SeuratObject merge.Assay SeuratObject merge.Seurat SeuratObject names.DimReduc SeuratObject names.Seurat SeuratObject print.DimReduc SeuratObject subset.Assay SeuratObject subset.DimReduc SeuratObject subset.Seurat SeuratObject Error in [[<-(*tmp*, "orig.ident", value = idents) : [[<- defined for objects of type "S4" only for subclasses of environment`

maddygriz commented 1 year ago

Hi @LuShuYangMing ,

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

Thanks, Maddy