Problem Creating a Seurat Object from a .rds file

[inenj]

I am following a tutorial online to create a custom reference dataset to annotate cells using downloaded data from this publication: https://www.nature.com/articles/s42003-020-0922-4

I downloaded the data from GEO using GSE130973.

I know this code has worked for others, but for some reason, it is throwing an error for me.

I have included the error output as a screenshot, but will also include it here:

RInterpreterError Traceback (most recent call last) Cell In[101], line 1 ----> 1 get_ipython().run_cell_magic('R', '-o healthy', 'seurat_object <- readRDS("ref_data/GSE130973_seurat_analysis_lyko.rds")\nseurat_object <- CreateSeuratObject(counts = assay(rse, "counts"), meta.data = as.data.frame(colData(rse)))\nhealthy <- as.SingleCellExperiment(seurat_object)\n')

File /Applications/anaconda3/lib/python3.12/site-packages/IPython/core/interactiveshell.py:2541, in InteractiveShell.run_cell_magic(self, magic_name, line, cell) 2539 with self.builtin_trap: 2540 args = (magic_arg_s, cell) -> 2541 result = fn(*args, **kwargs) 2543 # The code below prevents the output from being displayed 2544 # when using magics with decorator @output_can_be_silenced 2545 # when the last Python token in the expression is a ';'. 2546 if getattr(fn, magic.MAGIC_OUTPUT_CAN_BE_SILENCED, False):

File /Applications/anaconda3/lib/python3.12/site-packages/rpy2/ipython/rmagic.py:984, in RMagics.R(self, line, cell, local_ns) 982 if not e.stdout.endswith(e.err): 983 print(e.err) --> 984 raise e 985 finally: 986 if self.device in DEVICES_STATIC:

File /Applications/anaconda3/lib/python3.12/site-packages/rpy2/ipython/rmagic.py:949, in RMagics.R(self, line, cell, local_ns) 947 return_output = False 948 else: --> 949 text_result, result, visible = self.eval(code) 950 text_output += text_result 951 if visible:

File /Applications/anaconda3/lib/python3.12/site-packages/rpy2/ipython/rmagic.py:413, in RMagics.eval(self, code) 410 except (ri.embedded.RRuntimeError, ValueError) as exception: 411 # Otherwise next return seems to have copy of error. 412 warning_or_other_msg = self.flush() --> 413 raise RInterpreterError(code, str(exception), 414 warning_or_other_msg) 415 finally: 416 ro._print_deferred_warnings()

RInterpreterError: Failed to parse and evaluate line 'seurat_object <- readRDS("ref_data/GSE130973_seurat_analysis_lyko.rds")\nseurat_object <- CreateSeuratObject(counts = assay(rse, "counts"), meta.data = as.data.frame(colData(rse)))\nhealthy <- as.SingleCellExperiment(seurat_object)\n'. R error message: 'Error: unable to find an inherited method for function ‘assay’ for signature ‘x = "Seurat", i = "character"’'

%%R -o fibroblasts

seurat_object <- readRDS("ref_data/GSE130973_seurat_analysis_lyko.rds")

seurat_object <- CreateSeuratObject(counts = assay(rse, "counts"), meta.data = as.data.frame(colData(rse)))

fibroblasts <- as.SingleCellExperiment(seurat_object)

[samuel-marsh]

Hi,

So the issue is you are trying to use SCE commands (assay and colData) on Seurat object. You don't need to run:

seurat_object <- CreateSeuratObject(counts = assay(rse, "counts"), meta.data = as.data.frame(colData(rse)))

You can just read the rds file and then if you want SCE just run the as. SingleCellExperiment line that you have.

Best, Sam

[inenj]

Hi,

Thank you so much for helping me out. I'm still getting an error. I'm guessing it's because it doesn't contain the necessary annotation information I need to create a custom annotation reference. Thank you anyways.