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Table 1 Comparison of factors used for the LIMMA analyses of the same data set published in the Gaucher et al. [9]

From: VIO: ontology classification and study of vaccine responses given various experimental and analytical conditions

FactorOriginal analysisRe-analysis
FilteringFiltered probes with intensity below background
NormalizationQuantile normalization
TransformationLog2 transformation
Fold change cut-off< −1.3 or > 1.3
LIMMA versionUnspecified (before 2008)LIMMA 3.26.8
LIMMA SoftwareLIMMA package in BioconductorGEO2R
Multiple test correctionFalse discovery rate (FDR)
Adjusted p-value cut-off based on FDR0.05