We are analyzing metastatic samples that are metastasized to liver using 10x visium. Obviously , there will be adjacent normal liver liver tissue. While we are giving scRNA data from tumors , how will Cell2location annotate spots that have hepatocytes, satellite liver cells from normal liver. Will it ignore these spots ?
Thanks !
Hi @vibrant1984
cell2location will use the most similar cell types in your reference to explain RNA detected from normal liver tissue. You can always just run the analysis and see how it looks but keep the above in mind.