gravatar for el24

2 hours ago by

USA

Hi everyone,
I'm clustering my single-cell data using Scanpy package, and I use rank_gene_groups to rank genes for characterizing groups. This returns names, scores, logfoldchanges, pvals, and pvals_adj for my Anndata format. I'm trying to interpret logfoldchanges for this data, but I'm new to this field and I couldn't find any information except their source code. I saw explanations in this biostars post and I know what foldchange and logfoldchange mean, but I can't understand how to interpret this output. (using this resource)

"Fold change is calculated simply as the ratio of the difference between the final value and the initial value over the original value. Thus, if the initial value is A and the final value is B, the fold change is (B - A)/A or equivalently B/A - 1." But what does initial A and final B mean here in below output result from scanpy.tl.rank_gene_groups?

My second question is if you have any recommendations on how I can use this output to create a metric of how unique the genes are to a cluster? (fold enrichment of a gene in one cluster over the next highest cluster)

A couple of lines from my result is shown as follows. 0-n means the 'name' of cluster 0, followed by 'scores', 'pvals', and 'logfoldchanges' for cluter 0. Afterward, we have the same data for other clusters. (I have 5 clusters, but not all are shown in the image)

Screen-Shot-2020-04-30-at-00-36-31

Your help would be much appreciated! Thanks a lot in advance!

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2 hours ago
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el2410



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