SCDE for differential expression
Entering edit mode
mnaymik ▴ 10
Last seen 6.3 years ago
United States

I really like the approach taken in the SCDE package for single cell differential expression. In the examples differential expression analysis is performed between two cell types but would it be appropriate to use this package for differential expression in other scenarios? For example, all cell types at two time points? Or just cells of the same type at two time points? 


Cell type A, B, C  at T1  vs  A, B, C at T2


A at T1  vs  A at T2


Also, why is it that we get different results when running 

scde.expression.difference and scde.test.gene.expression.difference?

Here is an excerpt from their example:

##           lb     mle       ub       ce        Z       cZ
## Tdh 5.807793 8.075220 10.302866 5.807793 7.159589 5.989598
## Tdh 5.728235 8.03544 10.30287 5.728235 7.151425 7.151425


And with my data:

##           lb     mle       ub       ce        Z       cZ

EEF1A1          -1.304039   -1.188977   -1.112269   -1.112269   -7.160809   -7.160809

EEF1A1          -0.53693685   -0.421879   -0.3451737   -0.34517369   -7.160847   -6.123877    

scde differential expression single cell • 1.2k views

Login before adding your answer.

Traffic: 816 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