We found a match
Your institution may have access to this item. Find your institution then sign in to continue.
- Title
BatchQC: interactive software for evaluating sample and batch effects in genomic data.
- Authors
Manimaran, Solaiappan; Selby, Heather Marie; Okrah, Kwame; Ruberman, Claire; Leek, Jeffrey T.; Quackenbush, John; Haibe-Kains, Benjamin; Bravo, Hector Corrada; Johnson, W. Evan
- Abstract
Sequencing and microarray samples often are collected or processed in multiple batches or at different times. This often produces technical biases that can lead to incorrect results in the downstream analysis. There are several existing batch adjustment tools for '-omics' data, but they do not indicate a priori whether adjustment needs to be conducted or how correction should be applied. We present a software pipeline, BatchQC, which addresses these issues using interactive visualizations and statistics that evaluate the impact of batch effects in a genomic dataset. BatchQC can also apply existing adjustment tools and allow users to evaluate their benefits interactively. We used the BatchQC pipeline on both simulated and real data to demonstrate the effectiveness of this software toolkit.
- Subjects
NUCLEOTIDE sequence; PROTEIN analysis; GENETIC software; GENOMICS; BIOINFORMATICS
- Publication
Bioinformatics, 2016, Vol 32, Issue 24, p3836
- ISSN
1367-4803
- Publication type
Article
- DOI
10.1093/bioinformatics/btw538