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sunduanchen / Scissor

Scissor package
GNU General Public License v3.0
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About normalize bulk and sc data #29

Closed Ahawywyw closed 2 years ago

Ahawywyw commented 2 years ago

Hi! Thank you for the nice tools. In scissor, we use normalize.quantiles to normalize bulk and sc data. While I am wondering if we can normalize original bulk and sc count data.Thanks a lot!

sunduanchen commented 2 years ago

Hi,

For single-cell data, we recommend using some preprocessing steps in Seurat. It may not be applicable to perform quantile normalization on original count data.

Besides, I think you can even try other approaches to normalize original bulk and single-cell data separately. Different normalization approaches may have better performances in different applications.

We tried several normalizations and batch-effect removing techniques (such as function in 'combat' R packages) to explore Scissor's preliminary results. Finally, we used the quantile normalization in our tool since the corresponding results have more biologically meaningful cell subpopulations.

Hope these helps.

Best, Duanchen