从你的代码和运行上面看,并不是对应的啊~~~
你试试betaPrior=FALSE,具体为什么原因:
(整理来自SEQanswers)
I have a dataset where the condition of interest is a factor with 3 levels. DESeq2 issues me a warning to use betaPrior=False otherwise the log2 FoldChange will be affected by the base level. I thought the fold-change is always calculated w.r.t to a base level.
I tried to look in the DESeq2 paper at bioRXiv (http://biorxiv.org/content/early/2014/02/19/002832). In the paper, we say "logarithmic fold change prior", and as logarithmic fold changes are written as beta in the GLM, in the software we use the shorter "betaPrior".