TY - JOUR
T1 - Multiple testing corrections in quantitative proteomics
T2 - a useful but blunt tool
AU - Pascovici, Dana
AU - Handler, David C L
AU - Wu, Jemma X.
AU - Haynes, Paul A.
PY - 2016/9/1
Y1 - 2016/9/1
N2 - 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, most multiple 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.
AB - 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, most multiple 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.
UR - http://www.scopus.com/inward/record.url?scp=84988369559&partnerID=8YFLogxK
U2 - 10.1002/pmic.201600044
DO - 10.1002/pmic.201600044
M3 - Article
C2 - 27461997
AN - SCOPUS:84988369559
SN - 1615-9853
VL - 16
SP - 2448
EP - 2453
JO - Proteomics
JF - Proteomics
IS - 18
ER -