期刊
PROTEOMICS
卷 16, 期 18, 页码 2448-2453出版社
WILEY
DOI: 10.1002/pmic.201600044
关键词
FDR; Multiple testing corrections; Shot gun proteomics
资金
- BioPlatforms Australia through the Australian Government's National Collaborative Research Infrastructure Scheme
- Australian Research Council training centre for Molecular Technologies in the Food Industry
Multiple testing corrections are a useful tool for restricting the FDR, but can be blunt in the context of low power, as we demonstrate by a series of simple simulations. Unfortunately, in proteomics experiments low power can be common, driven by proteomics-specific issues like small effects due to ratio compression, and few replicates due to reagent high cost, instrument time availability and other issues; in such situations, mostmultiple testing corrections methods, if used with conventional thresholds, will fail to detect any true positives even when many exist. In this low power, medium scale situation, other methods such as effect size considerations or peptide-level calculations may be a more effective option, even if they do not offer the same theoretical guarantee of a low FDR. Thus, we aim to highlight in this article that proteomics presents some specific challenges to the standard multiple testing corrections methods, which should be employed as a useful tool but not be regarded as a required rubber stamp.
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