I am running analysis on RNA Seq data using DESeq2, I have two "treatments" for each sample each with two levels
status: sham or infected
temperature: high or low.
I have run the LRT to look at whether I am make sure I have not made any assumptions based on experimental design on whether genes are significantly dif expressed. To do this I have used the LRT
dstemp_lrt<-DESeq(dstemp, test="LRT", reduced= ~status)
log2 fold change (MLE): temperature L vs H
LRT p-value: '~ status + temperature' vs '~ status'
Am I correct in thinking that this gives the Pvalues of the genes significantly differentially expressed as a result of whether it was sham or infected in comparison to those genes sig. differentially expressed when temperature is also factored in (the interaction)?
Therefore I should also run with "reduced=~temperature" to test the same but with just temperature and then compare the two lists?