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kordastilab / ImmunoCluster

MIT License
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Error in reducedDim(indata, reducedDim)[, dimColnames] : no 'dimnames' attribute for array following CATALYST #9

Open denvercal1234GitHub opened 10 months ago

denvercal1234GitHub commented 10 months ago

Hi @JamesOpz,

Thank you for the package.

I had performed clustering and UMAP/TSNE through the CATALYST package but I hope to now use some plotting functions and the stat_test_clust for differential protein expression analyses of my clusters in the sce object.

However, I encountered error below. Would you mind letting me know if there are some conversion or manipulation of my object needed for compatibility with the immunoCluster?

Thank you for your help. 

### My sce object
> F37_channel_fcs_data_sce
class: SingleCellExperiment 
dim: 270 4955453 
metadata(5): experiment_info chs_by_fcs cluster_codes SOM_codes delta_area
assays(1): exprs
rownames(270): FSC.A FSC.H ... FlowSOM_cluster_backbone24 FlowSOM_metacluster_backbone24
rowData names(4): channel_name marker_name marker_class used_for_clustering
colnames: NULL
colData names(8): sample_id cell_count_prePeacoQC ... flowCore_postPeacoQC_medMFI_PE cluster_id
reducedDimNames(2): UMAP TSNE
mainExpName: NULL
altExpNames(0):