SMIXnorm: Fast and Accurate RNA-Seq Data Normalization for Formalin-Fixed Paraffin-Embedded Samples.

ABSTRACT: RNA-sequencing (RNA-seq) provides a comprehensive quantification of transcriptomic activities in biological samples. Formalin-Fixed Paraffin-Embedded (FFPE) samples are collected as part of routine clinical procedure, and are the most widely available biological sample format in medical research and patient care. Normalization is an essential step in RNA-seq data analysis. A number of normalization methods, though developed for RNA-seq data from fresh frozen (FF) samples, can be used with FFPE samples as well. The only extant normalization method specifically designed for FFPE RNA-seq data, MIXnorm, which has been shown to outperform the normalization methods, but at the cost of a complex mixture model and a high computational burden. It is therefore important to adapt MIXnorm for simplici

SUBMITTER: Yin S 

PROVIDER: S-EPMC8024626 | biostudies-literature | 2021

REPOSITORIES: biostudies-literature