Hello all!

I am working with a single-cell RNA seq dataset from 10x where I have two experimental conditions. Patients pre-treatment and post-treatment condition. I want to investigate the cell-type ratios differences between treatment stages. The main problem is that the number of cells sequenced/recovered in the pre-treatment stage is so low in comparison with the post-treatment stage. 

I was wondering, if exist a statistical method to "normalize" the number of cells recovered between conditions to compare the ratio in a reliable way. 


Regards
You can find a detailed discussion in the "Differential Abundance" Section of the OSCA book: [https://bioconductor.org/books/release/OSCA/multi-sample-comparisons.html#differential-abundance][1], especially the section about [Composition Effects](https://bioconductor.org/books/release/OSCA/multi-sample-comparisons.html#composition-effects) might be applicable to your situation. It would be important to have replicates of the conditions (which is generally recommended anyway).



  [1]: https://bioconductor.org/books/release/OSCA/multi-sample-comparisons.html#differential-abundance