error message for feature plot: Error in UseMethod(generic = "DefaultAssay", object = object) : no applicable method for 'DefaultAssay' applied to an object of class "character"

[wenjunatstanford]

I was able to do DimPlot for my object, and the metadata shows there are columns with data for nCount_RNA , nFeature_RNA etc., however, when I was trying to do FeaturePlot, somehow the error message consider my objects are "character". What should I do about this error message? thank you for your help!

Error in UseMethod(generic = "DefaultAssay", object = object) :
no applicable method for 'DefaultAssay' applied to an object of class "character"

[samuel-marsh]

@wenjunatstanford can you please provide full code you are running and output of sessionInfo()?

[wenjunatstanford]

Hi Samuel, I was able to get UMAP for my libraries and was trying to continue the analysis and get differential expressed genes in each cluster for different treatment. [cid:f7e37b5e-faf3-4926-ad7b-909bb7fb963e] I have recently downloaded the R version 4.5.0 and was trying to follow the instructions for differential expression analysis following the instruction https://satijalab.org/seurat/articles/integration_introduction.html#perform-integration-with-sctransform-normalized-datasets However, when I start the R studio I seem to have problems loading various libraries ( Please see attached below).

------------------ R version 4.5.0 (2025-04-11 ucrt) -- "How About a Twenty-Six" Copyright (C) 2025 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. Natural language support but running in an English locale R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. [Workspace loaded from ~/SnPAD/.RData]

library(Seurat)

Loading required package: SeuratObject Loading required package: sp Attaching package: ‘SeuratObject’ The following objects are masked from ‘package:base’: intersect, t Warning message: In readRDS(path) : error reading from connection

library(SeuratData)

Error in library(SeuratData) : there is no package called ‘SeuratData’

[cid:8538c365-dedd-44d7-8dd1-ea344ba172e9] What should I do from here? Thank you very much for your help! Wen-Jun

…

________________________________ From: Samuel Marsh ***@***.***> Sent: Saturday, May 10, 2025 3:28 PM To: satijalab/seurat ***@***.***> Cc: Wen-Jun Shen ***@***.***>; Mention ***@***.***> Subject: Re: [satijalab/seurat] error message for feature plot: Error in UseMethod(generic = "DefaultAssay", object = object) : no applicable method for 'DefaultAssay' applied to an object of class "character" (Discussion #9880) @wenjunatstanford<https://github.com/wenjunatstanford> can you please provide full code you are running and output of sessionInfo()? — Reply to this email directly, view it on GitHub<#9880 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/BSKH64YLYRJFFM5HSZA3G4D25Z4RNAVCNFSM6AAAAAB42CU6J2VHI2DSMVQWIX3LMV43URDJONRXK43TNFXW4Q3PNVWWK3TUHMYTGMJQGMZTQNQ>. You are receiving this because you were mentioned.