Entering edit mode
Hi,
My design looks like this ==I have 3 factors:
I'm interested to look at the effects of treatment(infection) on the gene expression in each organ over time. I'm having troubles understanding how to define the reduced model to run DESeq.
here is my code:
dds <- nbinomLRT(dds, full = ~Treatment + Organ + Time + Treatment:Time + Organ:Time, reduced = ~Treatment + Organ + Treatment:Time)
#rlog transformation
rld <- rlog(dds, blind=FALSE)
rld_mat <- assay(rld)
My questions:
- Are my full and reduced models correct for the intended purpose?
- Is my code for rlog transformation correct with "blind=FALSE" or should I use "blind=TRUE"?
Thanks!
Thanks.
Hi I was able to get an insight on the design. What is the difference in hypothesis testing between these two designs?
when I run both, there is a difference in the number of genes that are differentially expressed.
and
For questions about statistical analysis and interpretation, I recommend working with a local statistician or someone familiar with linear models in R.