scRNA-seq subclustering

Question

[miyeok]

Hi,

I'm doing single cell data analysis with controls and disease samples. and it turned out that an specific cell type "A" is increased in disease condition. then i wanted to re-clustering (subclustering) only the A cluster, so that i find out which specific cell subtype is affected by disease. and i finished that. But I have trouble interpreting cell proportional change of "A" subcluster.

in this case, do i have the set the denominator to All cell #? or only the "A" cell #?

Thank you

Answer 1

[Ming Tommy Tang]

You want to read this http://bioconductor.org/books/3.17/OSCA.multisample/differential-abundance.html

[miyeok]

Thank you so much!