I am trying to use the DESseq package to estimate ribosome loading efficiency as described in "systemPipeR Workflow for Ribo-Seq and polyRibo-Seq Experiments".
But I have run into some problems that I can't understand the genesis i.e.
"Error in nbinomLRT(object, full = full, reduced = reduced, betaPrior = betaPrior, :
less than one degree of freedom, perhaps full and reduced models are not in the correct order"
I have tried to look around the source of this error in the manpages but can't find it.
My colData looks like this:
DataFrame with 8 rows and 2 columns
M1A Ribo M1
M1B Ribo M1
A1A Ribo A1
A1B Ribo A1
V1A mRNA M1
V1B mRNA M1
M6A mRNA A1
M6B mRNA A1
with a datafile matching the colData row.names and as you can see every sample has a df>1
But when I run:
I get the above error message.
Is there something am missing?