search

satijalab / sctransform

R package for modeling single cell UMI expression data using regularized negative binomial regression
GNU General Public License v3.0
208 stars 33 forks source link

Inquiry about the batch correction model #162

Open jcho23 opened 1 year ago

jcho23 commented 1 year ago

Hi Christoph,

I am currently running the sctransform for my batch correction. It shows the batch model does not include the 'log_umi' variable in the linear model like below.

y ~ log_umi:batch + batch + 0

Can you please explain why your model does not include the 'log_umi' in the model like below?

y ~ log_umi + batch + log_umi:batch

It would be very helpful if you can answer it.

Thanks for your help in advance.