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theMILOlab / SPATA2

A Toolbox for Spatial Gene Expression Analysis
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Error runBayesSpaceClustering #100

Closed juliach2 closed 4 months ago

juliach2 commented 5 months ago

Hallo,

After denoising and plotting via plotSurface I run into an error when trying to cluster the data:

spata_obj <- runBayesSpaceClustering( object = spata_obj, name = "bayes_space" )

First I get the Error: Error in file(file, "rt") : cannot open the connection In addition: Warning message: In file(file, "rt") : cannot open file 'xx/outs/spatial/tissue_positions_list.csv': No such file or directory

As Space Ranger changed the name of tissue_positions_list.csv I changed the filename tissue_positions.csv to tissue_positions_list.csv manually.

After re-running I now get this error: Error in .subscript.2ary(x, , j, drop = TRUE) : subscript out of bounds

I tried it with my datasets, as well as the tutorial dataset.

I have the impression that it might be a problem with the changes in datastructure of seurat 5 as I get:

getGroupingOptions(spata_obj) factor factor factor factor "orig.ident" "Spatial_snn_res.0.8" "seurat_clusters" "histology"

I am using SPATA2 2.0.4 and Seurat 5.0.1. I tried to downgrade to seurat 4 but run ito the error reported in issue #99. Re-installing confuns did not fix it.

Is there a workaround?

Thank you!

kueckelj commented 5 months ago

Hello, actually I think it is a problem with the BayesSpace package itself. Can you try and create a SingleCell object with BayesSpace::readVisium() using the directory you used to create the spata2 object? Do you run into the same errors if you do so?

kueckelj commented 5 months ago

Can you reinstall SPATA2 and try again?

juliach2 commented 5 months ago

Thank you very much! Yes, with BayesSpace::readVisium() I got the same Error. After reinstalling SPATA2 the runBayesSpaceClustering() now works.

Unfortunatly I run into the next error using runSeuratClustering()

18:10:09 Using matrix 'scaled'. 18:10:09 Using expression matrix 'scaled'. Error in (function (cl, name, valueClass) : ‘scale.data’ ist kein Slot in Klasse “Assay5”

Could you please help again?