RNA-seq analysis without replicate

Question

[biology_inform]

Hi, I have a NGS data without a replicate and I need to analyze with EdgeR. In the UserGuide; 2.12 What to do if you have no replicates section says there are 2 ways with exactTest and glmFit. but I couldn't understand which one to use. How can I decide which one to use ?

[Kevin Blighe]

Gordon Smyth

Answer 1

[Gordon Smyth]

Actually the edgeR User's Guide gives four possible methods for analysing RNA-seq without replicates. The use of exactTest or glmLRT were just examples. There is no difference between the two in this context, either function could be used with any of the four methods.

[biology_inform]

Okay thanks. I also wonder the bcv <- 0.2 is like this in the user guide.

Typical values for the common BCV (square-rootdispersion) for datasets arising from well-controlled experiments are 0.4 for human data,
0.1 for data on genetically identical model organisms or 0.01 for technical replicates.

So I am identifiyng bcv as 0.4 since i am dealing with human data.

[Gordon Smyth]

Setting bcv <- 0.2 is just an example. As the passage you quote makes clear, 0.2 is well within the range of typical BCV values.