2.1. Microarray Data, Differential Expression Analysis
Public datasets from Gene Expression Omnibus (NCBI, Bethesda, MD, USA) were selected to investigate naphthalene effects on different organs/tissues. Experiment GSE18858 is about naphthalene exposure of mouse liver [19] and GSE17933 is about naphthalene exposure of mouse lung [20].
Raw data of naphthalene and control slides were normalized and background corrected using RMA (Robust Multi-array Average). The Limma (Linear Models for Microarray Data) method was applied to define fold changes of genes and adjusted p-values. The Limma (Linear Models for Microarray Data) method was applied to define fold changes of genes and to identify the significantly expressed genes using a Benjamini-Hochberg adjusted p-value cutoff (≤0.05) [21].