We found a match
Your institution may have access to this item. Find your institution then sign in to continue.
- Title
OSAT: a tool for sample-to-batch allocations in genomics experiments.
- Authors
Li Yan; Changxing Ma; Wang, Dan; Qiang Hu; Maochun Qin; Conroy, Jeffrey M.; Sucheston, Lara E.; Ambrosone, Christine B.; Johnson, Candace S.; Jianmin Wang; Song Liu
- 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.
- Subjects
BIOLOGICAL interfaces; GENOMICS; MOLECULAR genetics; GENETIC research; GENETICS
- Publication
BMC Genomics, 2012, Vol 13, Issue 1, p689
- ISSN
1471-2164
- Publication type
Article
- DOI
10.1186/1471-2164-13-689