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

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-fr

SUBMITTER: Acedo-Terrades A 

PROVIDER: S-EPMC11812149 | biostudies-literature | 2025 Feb

REPOSITORIES: biostudies-literature