Dear All,

I have two samples they are extracted from the same source at different times. What I want to do is to understand if inside at unsupervised analysis cluster this samples goes close.

In my hand at the moment both sample are not cluster together but they have a R^2 0f 0.94.

ddHTSeq <- DESeqDataSetFromHTSeqCount(sampleTable=SampleTable,directory="Count/", design= ~1)
dds <- DESeq(ddHTSeq)

 we do blind estimation once, then re-use these for both:
rld <- rlog(ddsblind, blind=FALSE)

## ----euclDist------------------------------------------------------------
sampleDists <- dist(t(assay(rld)))
sampleDists
hc =hclust(sampleDists,labels=metadata$CDT)

What do you think? Could be useful to delete all the counts gene are zero? Or maybe it is wrong the normalization methods I use