cummeRbund JS Distances (Jensen–Shannon divergence)

[puggie]

Has anyone used the cummerRbund bioconductor package on RNA-seq data?

How does one interpret the data?

I have 6 samples no replicates, of 2 different tissues. cummeRbund shows clear clustering of the samples tissue-specifically on a JS Distance scale.

The scale in my situation runs from 0 to 0.2.

So tissue 1 lies at 0,1
tissue 2 lies at 1,8

This is run on CuffDiff for a tissue-specific set of genes to tissue 1 known to be expressed from RTPCR and so on.

Then how do I interpret this? Clustering is clear, but why not 0.05 and 0.9 for the two groups? or something that tells that tissue 1 samples are 'close together'?

I hope this is not too trivial a question, and any comment is appreciated.

[andrikaa]

What is the difference, and what is the similarity. Can Javascript writer can write actionscipt ? and Can Actionscipt writer can work in javascript? Please Help. Confused by myself in both of them. Which would be better to learn.
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