Comparison of normalization and differential expression analyses using RNA-Seq data from 726 individual Drosophila melanogaster.

ABSTRACT:

Background

A generally accepted approach to the analysis of RNA-Seq read count data does not yet exist. We sequenced the mRNA of 726 individuals from the Drosophila Genetic Reference Panel in order to quantify differences in gene expression among single flies. One of our experimental goals was to identify the optimal analysis approach for the detection of differential gene expression among the factors we varied in the experiment: genotype, environment, sex, and their interactions. Here we evaluate three different filtering strategies, eight normalization methods, and two statistical approaches using our data set. We assessed differential gene expression among factors and performed a statistical power analysis using the eight biological replicates per genotype, environment, and sex

SUBMITTER: Lin Y 

PROVIDER: S-EPMC4702322 | biostudies-literature | 2016 Jan

REPOSITORIES: biostudies-literature