using limma and edgeR for differential expression of Drop-seq/10xGenomics scRNA-seq data
Entering edit mode
Bogdan ▴ 670
Last seen 4 months ago
Palo Alto, CA, USA

Dear Aaron, and all,

after going over the tutorial for detecting differential expression in scRNA-seq data


thought that I could ask you please :

would the same pipeline (that includes edgeR or limma) apply to scRNA-seq data from Drop-seq/10X Genomics ?

given the fact that the number of UMI reads per gene is very low (eg 0, 1, 2, 3, ...10, ... ; very few genes having 10-20 counts). thanks a lot !

-- bogdan

limma edgeR simplesingleCell scran scater • 2.7k views
Entering edit mode

You have to be more specific. What pipeline are you talking about? Are you referring to the marker gene detection? Or to the pseudo-bulk DE analysis?

Entering edit mode

Hi Aaron, thank you very much for your help and for the questions.

i was referring to "part 6 : Using pseudo-bulk counts" :

that describes the analysis on a SMART-seq2 dataset (416B cells).

It would be great to have again your insights and help. Thanks a lot !

Entering edit mode
Aaron Lun ★ 28k
Last seen 6 hours ago
The city by the bay

If you add the counts together to create the pseudo-bulk samples, they won't be low any more. So there's no problem if you have enough cells to contribute to the sum in each sample.

Even if you don't have many cells, edgeR would still be able to deal with low counts, provided the dispersion is low (< 0.5). Very high dispersions cause some of the approximations in the QL framework to fail.

If you have low counts and high dispersions, then this is the worst case scenario. edgeR will not be happy, but the same could be said for other methods, so there's not much that can be done here.

Entering edit mode

ok, wonderful, just wanted to double check and have a professional statistical advice ;)

thank you for writing a detailed documentation on assessing the differential expression.


Login before adding your answer.

Traffic: 891 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