difference between raw.embryo.time and embryo.time?

kimpenn / VisCello

Viscello for Visualization of Single Cell Data

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difference between raw.embryo.time and embryo.time? #10

Closed jc271828 closed 1 year ago

jc271828 commented 1 year ago

Hi,

I was wondering what's the difference between raw.embryo.time and embryo.time, in eset.rds@phenoData@data? I see they correlate well but are not exactly the same, and Packer et al. did Pearson correlation with an embryo bulk RNA-seq time-series and from there you guys "assigned" timepoints to cells. I wonder if embryo.time OR raw.embryo.time represents the "assigned" identity, and what's the meaning of the other one.

Thank you, J

qinzhu commented 1 year ago

Hi sorry for the delayed response. raw.embryo.time is time assigned based on correlating with bulk RNA-Seq, embryo.time is that time smoothed using the global umap.