recommended minimum cell numbers to pseudobulk for DE comparisons between groups
0
2
Entering edit mode
10 weeks ago
Sentinel156 ▴ 160

Dear all,

I have not been able to find any commentary on this so far so hoping for some help here.

What is a reasonable minimum number of cells per group for pseudobulking or for performing differential expression/Marker gene identification using MAST etc. I see in the muscat code (https://rdrr.io/bioc/muscat/f/vignettes/analysis.Rmd) a 10 cell minimum is used by default but I couldn't find any data behind this in the paper. Is this reasonable statistically?

Furthermore, any thoughts on best practises when comparing groups with a large discrepancy in cell number (e.g. 100 cells vs 1000+ cells)

I'm looking for some data investigating this if possible

Thanks in advance,

RNA-Seq scRNA single-cell • 185 views
ADD COMMENT
0
Entering edit mode

You can run a PCA on the pseudobulks to see whether number of cells is associated with variation between pseudobulk clusters. That anyway is a recommended strategy for any RNA-seq experiment, be it pseudobulk DE or just "normal" bulk RNA-seq. I have some more thoughts on this, maybe will find some time this evening to put together a proper answer.

ADD REPLY

Login before adding your answer.

Traffic: 2074 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