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constantAmateur / SoupX

R package to quantify and remove cell free mRNAs from droplet based scRNA-seq data
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Question about rho_c #121

Closed Hanxi-002 closed 1 year ago

Hanxi-002 commented 1 year ago

Hi there.

This isn't a question about running the package but about understanding the method. I wasn't sure where is more appropriate to ask. So thanks and apology in advance if this is the wrong forum for this.

I'm trying to understand the method a bit more and is having trouble understanding rho_c. In the paper, rho_c is given as a fraction of (\sumg n{g, c}) / (N_c \sum_g b_g). In the previous section, the authors stated that \sumg n{g, c} = N_c . So re-write rho_c to the following: (N_c) / (N_c \sum_g b_g). Since b_g is the fraction of gene g in all empty droplets. Then sum over all genes will lead to \sum_g b_g to 1.

Then rho_c would just always equal to 1.

I know I'm missing something here but I can't figure out what it is. Any help is appreciated. Thank you!!

constantAmateur commented 1 year ago

The key here is the next sentence after the equations, "where the sum is taken across all genes in cell c for which it is assumed mg, c = 0". So the sum in the equation for rho_c is not over all genes, but only those for which we assume m_g,c=0.