Search
Question: single-cells RNA-seq analysis by MAST with unbalanced group size
0
gravatar for shao
8 months ago by
shao80
Germany
shao80 wrote:

We have single-cells sequencing data from two groups of cells with 100 cells and 3000 cells, respectively. Our interest is to find the gene differentially expressed between these two groups, and we like to try MAST.

We are worrying abou the unbalanced group size, i.e, 100 vs 3000, will it affect the differential analysis, and how? Is there a way to attenuate the effect?

Thanks!

Shao

 

ADD COMMENTlink modified 8 months ago by Andrew_McDavid150 • written 8 months ago by shao80
1
gravatar for Andrew_McDavid
8 months ago by
Andrew_McDavid150 wrote:

Statistical validity is unaffected by the unbalanced group sizes.  Just like in an ANOVA or linear regression, the standard error of the estimate will account for the lower precision in the smaller group.  Unbalanced groups does reduce the statistical power, compared to an experiment with balanced groups (and the same overall N).  But 100 isn't such a small group in the first place, so I wouldn't be worried about it.

ADD COMMENTlink written 8 months ago by Andrew_McDavid150

To followup the question, I have one extreme case with only 3 cells in group 1 and 500 cells in group 2. Am I still on the safe side?  How should I estimate the minimal disparity in the sample sizes? I have other cases with 20 - 50 cells in group 1, and 500 cells in group 2.  Thank you. 

ADD REPLYlink modified 7 months ago • written 7 months ago by grl01030

Statistical validity (calibration of p-values) is unaffected by the unbalanced group sizes, but as above, power will be low.  Can you clarify what is meant by "minimal disparity in sample sizes?"

ADD REPLYlink written 7 months ago by Andrew_McDavid150
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.2.0
Traffic: 149 users visited in the last hour