title: Statistical strategies for microRNAseq batch effect reduction.
abstract: RNAseq technology is replacing microarray technology as the tool of choice for gene expression profiling. While providing much richer data than microarray, analysis of RNAseq data has been much more challenging. Among the many difficulties of RNAseq analysis, correctly adjusting for batch effect is a pivotal one for large-scale RNAseq based studies. The batch effect of RNAseq data is most obvious in microRNA (miRNA) sequencing studies. Using real miRNA sequencing (miRNAseq) data, we evaluated several batch removal techniques and discussed their effectiveness. We illustrate that by adjusting for batch effect, more reliable differentially expressed genes can be identified. Our study on batch effect in miRNAseq data can serve as a guideline for future miRNAseq studies that might contain batch effect.
authors.affiliation: Vanderbilt Ingram Cancer Center, Center for Quantitative Sciences, Nashville, TN 37232, USA.
authors.forename: Yan
authors.initials: Y
authors.lastname: Guo
authors.affiliation: Vanderbilt Ingram Cancer Center, Center for Quantitative Sciences, Nashville, TN 37232, USA.
authors.forename: Shilin
authors.initials: S
authors.lastname: Zhao
authors.affiliation: Department of Statistics, National Cheng Kung University, Tainan 70101, Taiwan.
authors.forename: Pei-Fang
authors.initials: PF
authors.lastname: Su
authors.affiliation: Department of Applied Mathematics, National Chiayi University, Chiayi 60004, Taiwan.
authors.forename: Chung-I
authors.initials: CI
authors.lastname: Li
authors.affiliation: Vanderbilt Ingram Cancer Center, Center for Quantitative Sciences, Nashville, TN 37232, USA.
authors.forename: Fei
authors.initials: F
authors.lastname: Ye
authors.affiliation: Vanderbilt Ingram Cancer Center, Center for Quantitative Sciences, Nashville, TN 37232, USA.
authors.forename: Charles R
authors.initials: CR
authors.lastname: Flynn
authors.affiliation: Vanderbilt Ingram Cancer Center, Center for Quantitative Sciences, Nashville, TN 37232, USA.
authors.forename: Yu
authors.initials: Y
authors.lastname: Shyr
keywords: batch effect removal; miRNA sequencing; normalization