correlation method of cluster annotation

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BigOmics Analytics Team

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Aug 31, 2021, 5:04:04 AMAug 31
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I have a question regarding the correlation coefficient "R" mentioned in the cluster annotation under the section "clustering". I was wondering which correlation method was used to determine this coefficient?

[Thorben S., 19.08.2021]

BigOmics Analytics Team

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Aug 31, 2021, 5:10:20 AMAug 31
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We use the Spearman's rank correlation for the calculation which is calculated as the Pearsons correlation on the ranks. For the genesets, we take the average relative log expression for the genes in the genesets as geneset expression value. Notice that p-value are not computed in this module. We could technically do that (computing p-value for correlation) but it would slow down the module considerably. For more traditional geneset enrichment and p-value, the user should use the geneset enrichment module under the "Enrichment" menu.

Ivo
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