TY - JOUR
T1 - BatchQC
T2 - Interactive software for evaluating sample and batch effects in genomic data
AU - Manimaran, Solaiappan
AU - Selby, Heather Marie
AU - Okrah, Kwame
AU - Ruberman, Claire
AU - Leek, Jeffrey T.
AU - Quackenbush, John
AU - Haibe-Kains, Benjamin
AU - Bravo, Hector Corrada
AU - Evan Johnson, W.
N1 - Funding Information:
This research was supported by funds from the National Institutes of Health (R01 HG005692, R01 ES025002), and the National Science Foundation (DGE 0654108).
Publisher Copyright:
© The Author 2016. Published by Oxford University Press.
PY - 2016/12/15
Y1 - 2016/12/15
N2 - 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.
AB - 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.
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U2 - 10.1093/bioinformatics/btw538
DO - 10.1093/bioinformatics/btw538
M3 - Article
C2 - 27540268
AN - SCOPUS:85027499753
SN - 1367-4803
VL - 32
SP - 3836
EP - 3838
JO - Bioinformatics
JF - Bioinformatics
IS - 24
ER -