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EngeLab / CIMseq

Cell Interaction by Multiplet Sequencing (CIM-Seq) uses computational deconvolution of RNA-seq data from partially dissociated tissue to create cell interaction maps.
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‘NA’ values in calculateEdgeStats output #50

Open diyang1354 opened 3 years ago

diyang1354 commented 3 years ago

Dear author: I used droplet based method to generate the data, and followed the vignette. However, calculateEdgeStats returns a tibble with 'NA' values. What might be the problem? Thanks. image

My arguments to generate CIMseqSinglets object:

  1. count matrix: 2000 variable genes x N singlets umi matrix
  2. ERCC matrix: matrix( )
  3. dim.reduction: 2 column UMAP representation
  4. cell class My arguments to generate CIMseqMultiplets object:
  5. count matrix: 2000 variable genes in singlet dataset x N multipltes umi matrix
  6. ERCC matrix: matrix( )
  7. selected feature index: 1:2000

sObj generated by CIMseqSwarm looks like: image

EngeLab commented 3 years ago

It could be that CIMseq detects no heterotypic multiplets at all, which might result in this type of error. Is the "weight" column from calculateEdgeStats all zeros? This column indicates the number of times the "from"-"to" interaction appeared in the data, so if it is 0 it means no multiplets with that combination of cells was detected.

If possible, can you send me the Swarm object so I can check?

Best, Martin