How to statistically test the separation of two clusters in PCA
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5 months ago
bright602 ▴ 40

Hi, I am using the dba.plotPCA function in DiffBind to get a PCA plot. Could someone tell me how to use the statistic test to test the separation between two clusters? If possible, could I add the 95% CI ellipses in dba.plotPCA function? Thanks a lot for your help!

ChIP-Seq DiffBind • 264 views
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What will you testing? What statement do you wish to be 95% confident about?

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I am trying to know whether the two clusters are separated enough. Visually they are, but I just want to add some stats power. If not easily achieve, I am thinking to mark the 95% CI ellipses and illustrate the degree of overlapping/separation.

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That's just a repeat of what you already said. 95% CI on what, exactly? For example, in a t-test, the confidence interval is for the difference in mean between the two populations being tested. A PCA is a tool to reduce dimensionality - I don't think it tests any hypotheses to give you confidence intervals.

I'm sorry - I did not understand your question well. Does this SO post help: https://stackoverflow.com/questions/13936051/adding-ellipses-to-a-principal-component-analysis-pca-plot

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Thank you for your help.

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Thanks a lot Alex for the links!

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I think there is some discussion about CIs in relation to information measures. Hope it helps.

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