I have a 2x2 design, below is the piece of R code"

dds <- DESeq(ddsHTseq)
resultsNames(dds)

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?

hi yg,

I don't have any recommendation for you. My best advice is to consult locally with the experimentalists and maybe others who have analyzed sequencing data at your facility.