The immune-deconv analysis README.md currently describes the xCell method we use to deconvolute immune cell types, and indicates xCell scores can be compared across samples AND across cell types. This description is not accurate, as is indicated in here. Moreover, this method is technically not a deconvolution method, but it is actually signature-based as indicated in the xCell paper
In addition, we also compared xCell’s performance on test mixtures with that of CIBERSORT, a prominent deconvolution-based method [7]. Unlike signature-based methods, which output independent enrichment scores per cell type, the output from deconvolution-based methods is the inferred proportions of the cell types in the mixture.
What changes need to be made? Please provide enough detail for another participant to make the update.
The README itself needs to be updated. One important question is whether, given this information, xCell still meets our analysis goals.
sjspielman
commented
2 years ago
What analysis module should be updated and why?
The
immune-deconvanalysis README.md currently describes the xCell method we use to deconvolute immune cell types, and indicates xCell scores can be compared across samples AND across cell types. This description is not accurate, as is indicated in here. Moreover, this method is technically not a deconvolution method, but it is actually signature-based as indicated in the xCell paperWhat changes need to be made? Please provide enough detail for another participant to make the update.
The README itself needs to be updated. One important question is whether, given this information, xCell still meets our analysis goals.
Who will complete the updated analysis?
@sjspielman