Hi everyone. I have a question on using edgeR to analyze time series data. How to choose the degree of freedom when making design matrix? I basically follow the manual section 4.8 Time course RNA-seq experiments of Drosophila melanogaster to do the analysis;
My sample is here, a 6 time points experiment without replicates. I want to compare specific time effect
Hours <- c(0,1,2,4,8,16) Time <- paste0(Hours,"hrs") y <- DGEList(counts=x, group = Time)
To create a design matrix, both
ns() need a degree of freedom. I'm new to this field, what value should I use here?
I also find that in the later part 4.8.8 Time course trend analysis, it says that "We test for a trend by conducting F-tests on 3 df for each gene:", does this df in F-test relate to the design matrix one?