The importance of data transformation in RNA-Seq preprocessing for bladder cancer subtyping

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• dc.contributor.author Acedo-Terrades, Ariadna
• dc.contributor.author Perera Bel, Júlia
• dc.contributor.author Nonell Mazelon, Lara, 1972-
• dc.date.accessioned 2025-10-21T18:06:52Z
• dc.date.available 2025-10-21T18:06:52Z
• dc.date.issued 2025
• dc.date.updated 2025-10-21T18:06:51Z
• dc.description.abstract Objective: RNA-Seq provides an accurate quantification of gene expression levels and it is widely used for molecular subtype classification in cancer, with special importance in prognosis. However, the reliability and validity of these analyses can significantly be influenced by how data are processed. In this study we evaluate how RNA-Seq preprocessing methods influence molecular subtype classification in bladder cancer. By benchmarking various aligners, quantifiers and methods of normalization and transformation, we stress the importance of preprocessing choices for accurate and consistent subtype classification. Results: Our findings highlight that log-transformation plays a crucial role in centroid-based classifiers such as consensusMIBC and TCGAclas, while distribution-free algorithms like LundTax offer robustness to preprocessing variations. Non log-transformed data resulted in low classification rates and poor agreement with reference classifications in consensusMIBC and TCGAclas classifiers. Additionally, LundTax consistently demonstrated better separation among subtypes, compared to consensusMIBC and TCGAclas, regardless of preprocessing methods. Nonetheless, the study is limited by the lack of a true reference for objective assessment of the accuracy of the assigned subtypes. Hence, future work will be necessary to determine the robustness and scalability of the obtained results.
• dc.format.mimetype application/pdf
• dc.identifier.citation Acedo-Terrades A, Perera-Bel J, Nonell L. The importance of data transformation in RNA-Seq preprocessing for bladder cancer subtyping. BMC Res Notes. 2025 Feb 10;18(1):61. DOI: 10.1186/s13104-025-07138-x
• dc.identifier.doi http://dx.doi.org/10.1186/s13104-025-07138-x
• dc.identifier.issn 1756-0500
• dc.identifier.uri http://hdl.handle.net/10230/71619
• dc.language.iso eng
• dc.publisher BioMed Central
• dc.relation.ispartof BMC Research Notes. 2025;18(1):61
• dc.rights © The Author(s) 2025. Open Access This article is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License, which permits any non-commercial use, sharing, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if you modified the licensed material. You do not have permission under this licence to share adapted material derived from this article or parts of it. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by-nc-nd/4.0/.
• dc.rights.accessRights info:eu-repo/semantics/openAccess
• dc.rights.uri http://creativecommons.org/licenses/by-nc-nd/4.0/
• dc.subject.keyword Bladder cancer
• dc.subject.keyword Molecular subtypes
• dc.subject.keyword Preprocessing
• dc.subject.keyword RNA sequencing
• dc.title The importance of data transformation in RNA-Seq preprocessing for bladder cancer subtyping
• dc.type info:eu-repo/semantics/article
• dc.type.version info:eu-repo/semantics/publishedVersion