Hi,
I am new to analyze the RNAseq data. I have 6 samples (3 Controls and 3 treated) for which I would like to find how similar/dissimilar are they.
I found the similarity/dissimilarity between samples using Eucledian distance as well as Correlation matrix but the resulting dendogram are different between this two methods. I cant understand why this is happening. Kindly guide me.
Code for heatmap based on Euclidean Distance
Code for Correlation heatmap
I am new to analyze the RNAseq data. I have 6 samples (3 Controls and 3 treated) for which I would like to find how similar/dissimilar are they.
I found the similarity/dissimilarity between samples using Eucledian distance as well as Correlation matrix but the resulting dendogram are different between this two methods. I cant understand why this is happening. Kindly guide me.
Code for heatmap based on Euclidean Distance
Code:
vsd <- varianceStabilizingTransformation(dds, blind=TRUE) heatmap(as.matrix(dist(t(assay(vsd)))))
Code:
heatmap(cor(assay(vsd)))
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