Question: Rnaseq correlation between two samples
gravatar for jack1
5.6 years ago by
jack110 wrote:

Dear All,


I have two sample they  are extracted from the same source at  different time. 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 togheter 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)))
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

rna-seq deseq2 • 2.0k views
ADD COMMENTlink modified 5.6 years ago by Devon Ryan95k • written 5.6 years ago by jack110

How close/distant any given samples will be after clustering is dependent on the other samples present. Do you only have these two samples in the dataset? If not, it'd be impossible for them to cluster together unless all of their normalized values were identical.

ADD REPLYlink modified 5.6 years ago • written 5.6 years ago by Devon Ryan95k
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