How to perform deconvolution with RPKM values

[chenming9453]

Hi Xuran,

I tried to apply MuSiC to RNAseq bulk data with RPKM as the input. According to your paper(Discussion), "MuSiC can utilize RPKM if estimates of cell type-specific total RNA abundance can be provided." I am wondering how I can incorporate cell-type-specific total RNA abundance into your function? Or can I directly use RPKM as the input and use music_prop to do the deconvolution? Does my reference single-cell RNAseq data also requires RPKM as the input? Thanks!

Best, Ming

[zhanglab2008]

I brought up this thread since I also have the same question. A lot of people only make RPKM count matrices available to download from GEO so it will be hugely helpful if the MuSiC author can provide a way to analyze the RPKM file. Many thanks!