How to assess which cell population is most affected by treatmant in single cell rna seq data?
Entering edit mode
8 days ago
abbas89 ▴ 10

Hi, I have a single cell RNA seq dataset where I have several samples either control or treated, these samples contain several populations. I want to assess which cell population is most affected by the treatment. To give you an idea, I thought to: 1- Identify the highly variable genes. 2- For each group (control vs treated) compute the average expression of each pupulation for each of the variable genes. 3- For each cell population, compute the sum of the Log FC of the variable genes, let's name this: SFC The cell population with the highest SFC is the one most affected by the treatment. If cell population A is not affected by the treatment, SFC would be close to zero as ; the log FC for all the variable genes in treated vs control would be 0.

Is it a correct way to assess how much the treatment affects each population and do you have other ideas to achieve this? Thanks

transcriptomics single-cell RNA DEG • 257 views

Login before adding your answer.

Traffic: 1088 users visited in the last hour
Help About
Access RSS

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

Powered by the version 2.3.6