MIXnorm: normalizing RNA-seq data from formalin-fixed paraffin-embedded samples.

ABSTRACT:

Motivation

Recent studies have shown that RNA-sequencing (RNA-seq) can be used to measure mRNA of sufficient quality extracted from formalin-fixed paraffin-embedded (FFPE) tissues to provide whole-genome transcriptome analysis. However, little attention has been given to the normalization of FFPE RNA-seq data, a key step that adjusts for unwanted biological and technical effects that can bias the signal of interest. Existing methods, developed based on fresh-frozen or similar-type samples, may cause suboptimal performance.

Results

We proposed a new normalization method, labeled MIXnorm, for FFPE RNA-seq data. MIXnorm relies on a two-component mixture model, which models non-expressed genes by zero-inflated Poisson distributions and models expressed genes by truncated normal

SUBMITTER: Yin S 

PROVIDER: S-EPMC7267832 | biostudies-literature | 2020 Jun

REPOSITORIES: biostudies-literature