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JEFworks / ubit2

User-friendly Bioinformatics Tools
http://pklab.med.harvard.edu/jean/ubit2/index.html
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different results upon reload? #4

Closed ngehlenborg closed 8 years ago

ngehlenborg commented 8 years ago

Every time I reload the page I get different results (without changing anything). Is that intentional?

JEFworks commented 8 years ago

There's some stochasticity in the k-means clustering. Currently, k-means clustering is used to identify 2 main "subpopulations" in the data. If the k-means clusters change, then the PCA colorings will change, and all the downstream differential expression analysis (p-value, fold-change, and volcano plot) will change. Since the heatmap columns are sorted by fold change, the row ordering changes.

I was considering getting rid of the k-means clustering and just using a cutree(k=2) equivalent on the hierarchical clustering. Alternatively, if there's a way to set a random seed via Javascript, that could work too. Do you have any recommendations?

ngehlenborg commented 8 years ago

Could you store the results of the k-means clustering in localStorage or sessionStorage and only rerun the k-means when the data changes?

JEFworks commented 8 years ago

I haven't yet figure out how to best use localStorage or sessionStorage since both require strings rather than objects. The latest commit https://github.com/JEFworks/ubit2/commit/3c19e62fba46d2ec99559a9be582cd0ea7e4bb83 allows each panel to be run separately, so users can keep the k-means clustering they have while re-running the hierarchical clustering analysis for example.

slowkow commented 8 years ago

Consider trying localForage to store results in the user's browser.