Question: clustering from breast cancer RNA-seq data
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gravatar for silviajserrano
3.9 years ago by
silviajserrano40 wrote:

Hello!! I work in breast cancer and I have RNA-seq data from 60 patients. I classified the samples into intrinsic subtypes by immunohistochemistry and I have been using DEseq2 to perform differentially expression analysis between subtypes. I would like to do a global analysis. I mean, I would like to see which samples cluster together according to the gene expression, something unsupervised but using the whole transcriptome. I already used PAM50 to assign samples into intrinsic subtypes according to gene expression but I would like to see what samples cluster together and what characterized each cluster and from there I would like to do the differentially expression analysis…what tools can I use?

rna-seq • 2.2k views
ADD COMMENTlink modified 3 months ago by skjobs012370 • written 3.9 years ago by silviajserrano40
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gravatar for Michael Love
3.9 years ago by
Michael Love1.9k
United States
Michael Love1.9k wrote:

Have you seen the clustering examples in the DESeq2 vignette or workflow?

vignette("DESeq2")

For 60 samples, I would apply the varianceStabilizingTransformation (see vignette), then explore with the plots we show in the vignette. You can use built in R tools to cluster, for example:

mat <- assay(vsd)
hc <- hclust(dist(t(mat)))
plot(hc)
cutree(hc, k=3)

If you get the latest version of R (3.3) and the latest version of DESeq2 (1.12) you can use an even faster version of VST I just implemented:

vsd <- vst(dds)
ADD COMMENTlink written 3.9 years ago by Michael Love1.9k
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gravatar for silviajserrano
3.9 years ago by
silviajserrano40 wrote:

Thank you!! and after clustering, How can I explore the gene expression of each cluster? I mean, what characterize each cluster...

ADD COMMENTlink written 3.9 years ago by silviajserrano40
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gravatar for skjobs0123
3 months ago by
skjobs012370
skjobs012370 wrote:

For the RNA seq or higher dimensional matrix, I will recommend you to use the tSNE algorithm for unsupervised clustering i.e. PCA.

ADD COMMENTlink written 3 months ago by skjobs012370
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