Calculating percentage of cells proliferating in single cell rna seq data
0
0
Entering edit mode
3 months ago
mropri ▴ 150

Hi,

I have proliferation score for each cell for multiple samples including one control sample. I want to determine what percentage of cells relative to control cells are proliferating in my treatment sample. Is there any suggestions on how to proceed. My thought was to use the Otsu method to find an objective threshold for each sample based on the proliferation score for cells within that sample. This would find a proliferation score threshold that would divide the cells into two groups, proliferating vs non proliferating. Then I can calculate the percentage of cells within that sample that are proliferating. I can do this for each sample including control and compare the percentages of cells proliferating in my treatment samples to the control. Does this sound reasonable or is there a better way to approach this. Appreciate any thoughts.

statistics scRNA-seq proliferation • 404 views
ADD COMMENT
0
Entering edit mode

I would also visualize "the scores", stratified by sample, cell type, basically whatever feature that might be of interest. This can help you to set/review thresholds.

ADD REPLY
0
Entering edit mode

Thank you for your reply. I have the cell types annotated and then for each cell type I have the proliferation scores for each sample. My question is, is the otsu method fine for finding the threshold for each cell type within each sample and then calculating the proportion of cells above that threshold as proliferating. Doing this for each sample to get a percentage of proliferating cells and compare that across samples or is there another statistical way to go about this.

ADD REPLY
0
Entering edit mode

i have a same problem! have you done it? how about the effect? could you share your code with me? thank you very much!!!

ADD REPLY

Login before adding your answer.

Traffic: 3333 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6