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Question: Subsequent analysis after PCA and sample distance matrix-Outliers?
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gravatar for yg
2.4 years ago by
yg0
United States
yg0 wrote:

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?

 

ADD COMMENTlink modified 2.4 years ago by Michael Love13k • written 2.4 years ago by yg0
0
gravatar for Michael Love
2.4 years ago by
Michael Love13k
United States
Michael Love13k wrote:

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.

ADD COMMENTlink written 2.4 years ago by Michael Love13k
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