1. Normalization of RNA-Seq data using adaptive trimmed mean with multi-reference.
- Author
-
Singh, Vikas, Kirtipal, Nikhil, Song, Byeongsop, and Lee, Sunjae
- Subjects
- *
RECEIVER operating characteristic curves , *RNA sequencing - Abstract
The normalization of RNA sequencing data is a primary step for downstream analysis. The most popular method used for the normalization is the trimmed mean of M values (TMM) and DESeq. The TMM tries to trim away extreme log fold changes of the data to normalize the raw read counts based on the remaining non-deferentially expressed genes. However, the major problem with the TMM is that the values of trimming factor M are heuristic. This paper tries to estimate the adaptive value of M in TMM based on Jaeckel's Estimator, and each sample acts as a reference to find the scale factor of each sample. The presented approach is validated on SEQC, MAQC2, MAQC3, PICKRELL and two simulated datasets with two-group and three-group conditions by varying the percentage of differential expression and the number of replicates. The performance of the present approach is compared with various state-of-the-art methods, and it is better in terms of area under the receiver operating characteristic curve and differential expression. [ABSTRACT FROM AUTHOR]
- Published
- 2024
- Full Text
- View/download PDF