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dtsoucas / DWLS

Gene expression deconvolution using dampened weighted least squares

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bulk normalization methods

qingnanl opened this issue · comments

commented

Dear DWLS team,

Thanks for making the package. I am interested in what bulk RNA-seq normalization method could be used for this package. In the paper, I noticed that you all used FPKM for bulk. You also mentioned that the single-cell normalization is critical. For bulk, have you tested other normalizations, such as raw counts or TPM/CPM?

Thanks,

qingnan

commented

We have not tried other approaches, but would be curious to know how performance changes using other bulk normalization approaches.