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dmcable / spacexr

Spatial-eXpression-R: Cell type identification (including cell type mixtures) and cell type-specific differential expression for spatial transcriptomics
GNU General Public License v3.0
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Incorporate Spotclean results with RCTD #199

Open ayusyarif opened 7 months ago

ayusyarif commented 7 months ago

Hi,

I tried to remove the bleeding effect using the SpotClean package and generated an adjusted normalized matrix containing non-integer values. I want to use this matrix as the input for the RCTD analysis. Is there a way to modify this within the runRCTD function, or has somebody already tried this?

Thank you

Best, Ayu

ahwanpandey commented 2 months ago

I saw a similar issue being answered here

https://github.com/dmcable/spacexr/issues/147

@ayusyarif what did you end up doing? I am thinking of rounding the values into integers first.