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Yelab2020 / Cottrazm

Construct Tumor Transition Zone Microenvironment
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Error while reading the input file #11

Closed Kislai closed 7 months ago

Kislai commented 7 months ago

Hi,

Thank you developing this package. I have been trying to use the package and have been facing error in the preprocessing step itself.

I get the error even when I use the trial data of the package [Error in initialize(value, ...) : invalid name for slot of class "Assay5": min.spots]

When I put the input directory path to one of the public data set that I am trying to analyze, it doesn't recognize the .h5 file. [Error in Seurat::Read10X_h5(filename = paste(InDir, "filtered_feature_bc_matrix.h5", :File not found]

However, the file can be read with the same path name in other function eg. Load10X_Spatial It would be great if you can help me here!

Please find the attachment for the analysis steps and SessionInfo. Cottrazm_Error.txt

Kislai commented 7 months ago

Figured out that Cottrazm isn't compatible with Seurat v5. It worked when the older version of Seurat was installed [Version 4.4.0]. Closed the issue.