title: OSAT: a tool for sample-to-batch allocations in genomics experiments.
abstract: BACKGROUND
  Batch effect is one type of variability that is not of primary interest but ubiquitous in sizable genomic experiments. To minimize the impact of batch effects, an ideal experiment design should ensure the even distribution of biological groups and confounding factors across batches. However, due to the practical complications, the availability of the final collection of samples in genomics study might be unbalanced and incomplete, which, without appropriate attention in sample-to-batch allocation, could lead to drastic batch effects. Therefore, it is necessary to develop effective and handy tool to assign collected samples across batches in an appropriate way in order to minimize the impact of batch effects.
  
  
  RESULTS
  We describe OSAT (Optimal Sample Assignment Tool), a bioconductor package designed for automated sample-to-batch allocations in genomics experiments.
  
  
  CONCLUSIONS
  OSAT is developed to facilitate the allocation of collected samples to different batches in genomics study. Through optimizing the even distribution of samples in groups of biological interest into different batches, it can reduce the confounding or correlation between batches and the biological variables of interest. It can also optimize the homogeneous distribution of confounding factors across batches. It can handle challenging instances where incomplete and unbalanced sample collections are involved as well as ideally balanced designs.
authors.affiliation: Department of Biostatistics and Bioinformatics, Roswell Park Cancer Institute, Buffalo, NY 14263, USA. Li.Yan@RoswellPark.org
authors.forename: Li
authors.initials: L
authors.lastname: Yan
authors.forename: Changxing
authors.initials: C
authors.lastname: Ma
authors.forename: Dan
authors.initials: D
authors.lastname: Wang
authors.forename: Qiang
authors.initials: Q
authors.lastname: Hu
authors.forename: Maochun
authors.initials: M
authors.lastname: Qin
authors.forename: Jeffrey M
authors.initials: JM
authors.lastname: Conroy
authors.forename: Lara E
authors.initials: LE
authors.lastname: Sucheston
authors.forename: Christine B
authors.initials: CB
authors.lastname: Ambrosone
authors.forename: Candace S
authors.initials: CS
authors.lastname: Johnson
authors.forename: Jianmin
authors.initials: J
authors.lastname: Wang
authors.forename: Song
authors.initials: S
authors.lastname: Liu
mesh_terms: D000465:Algorithms; D003625:Data Collection / Q000379:methods*; D023281:Genomics / Q000379:methods*; D012984:Software