I have a 2x2 design, below is the piece of R code"
dds <- DESeq(ddsHTseq)
rld <- rlog(dds)
plotPCA(rld, intgroup=c("condition", "group"))
However, I found two samples within the same group was quite apart , the sample distance matrix is even worse: samples under the same condition didn't group together, does this mean I have outliers? If so, which samples should be considered outliers?