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Nonetheless, all subtype correlations are required to build the risk of recurrence (ROR) score, currently used in therapeutic decisions. Present subtype uncertainty estimations are not accurate, seldom considered or require a population-based approach for this context.<\/jats:p><\/jats:sec><jats:sec><jats:title>Results<\/jats:title><jats:p>Here we present a novel single-subject non-parametric uncertainty estimation based on PAM50\u2019s gene label permutations. Simulations results (n\u2009=\u20095228) showed that only 61% subjects can be reliably \u2018Assigned\u2019 to the PAM50 subtype, whereas 33% should be \u2018Not Assigned\u2019 (NA), leaving the rest to tight \u2018Ambiguous\u2019 correlations between subtypes. The NA subjects exclusion from the analysis improved survival subtype curves discrimination yielding a higher proportion of low and high ROR values. Conversely, all NA subjects showed similar survival behaviour regardless of the original PAM50 assignment. We propose to incorporate our PAM50 uncertainty estimation to support therapeutic decisions.<\/jats:p><\/jats:sec><jats:sec><jats:title>Availability and Implementation<\/jats:title><jats:p>Source code can be found in \u2018pbcmc\u2019 R package at Bioconductor.<\/jats:p><\/jats:sec><jats:sec><jats:title>Supplementary information<\/jats:title><jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p><\/jats:sec>","DOI":"10.1093\/bioinformatics\/btw704","type":"journal-article","created":{"date-parts":[[2016,11,4]],"date-time":"2016-11-04T20:05:38Z","timestamp":1478289938000},"page":"693-700","source":"Crossref","is-referenced-by-count":15,"title":["A novel non-parametric method for uncertainty evaluation of correlation-based molecular signatures: its application on PAM50 algorithm"],"prefix":"10.1093","volume":"33","author":[{"given":"Crist\u00f3bal","family":"Fresno","sequence":"first","affiliation":[{"name":"UA AREA CS. AGR. ING. BIO. 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