Determining the divergence between samples
I've been trying to reproduce this in Dana Pe'er's analysis software Cyt(Sightof). I made viSNE maps of two very different samples (sample A and sample B)
and use the 'compare maps' option in cyt as indicated in the Cytutorial.ppt.
In the window that pops up I can however only select the viSNE maps of one file, and not compare two files to each other.
Hence, I've tried to compare the viSNE map of sample A to the viSNE map generated from both sample A and sample B, but the divergence score is only ~0.1 even though the viSNE maps show no overlap between sample A and B; so that is clearly not the way to do it.
The paper 'supplementary figure 5 A' shows 3 marrow donors; clearly one viSNE was generated on all three marrows and then the JS divergence was calculated (where they conclude the samples are highly similar with a divergence of ~0.04). I thought they used Cyt, but I'm starting to doubt that now..
My question is, does anyone know how to determine the similarity between two samples through viSNE or other means (without knowing much about R...)?
Thanks for your time,
Ron