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Nanostring-Biostats / SpatialDecon

The SpatialDecon library implements the SpatialDecon algorithm for mixed cell deconvolution in spatial gene expression datasets. (This algorithm also works in bulk expression profiling data.)
MIT License
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usage of the cell abundance scores #5

Open cjhong opened 3 years ago

cjhong commented 3 years ago

I would like to use the estimated cell abundance from res$beta.

Can I use these cell abundance scores to compare across multiple samples?

Can I use these cell abundance scores between cell-types in a patient sample?

Thank you!

patrickjdanaher commented 3 years ago

Can I use these cell abundance scores to compare across multiple samples?

yes! Can I use these cell abundance scores between cell-types in a patient sample? yes, but with less certainty. This comparison depends on the columns of the cell profile matrix correctly representing the total RNA content in each cell type. We have made every effort to ensure this with the safeTME, but our solution is undoubtedly imperfect.