negative expression after cell cycle correction

[icanwinwyz]

Hi
This is Joe from Cedars-Sinai Medical Center. I am currently using your scLVM on single cell RNA-seq data to reduce the cell cycle effect. This is a very nice pipeline on single cell data analysis! So far, everything goes very well and no error message pop out by following your R tutorials. However, when I checked the gene expression after cell cycle correction, I found some of the genes have negative value of expression. I also used your demo data (Mouse T cells) to run the scLVM pipeline and also found the negative value after cell cycle correction. We know gene expression would never be negative, so my question is how to interpret this negative value? Thanks.

Looking forwards to your reply.

Joe

[BinDuan]

I have the same question that lots of genes have negative value of expression after cell cycle correction. Is that normal?