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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

Factor Original analysis Re-analysis
Filtering Filtered probes with intensity below background
Normalization Quantile normalization
Transformation Log2 transformation
Fold change cut-off < −1.3 or > 1.3
LIMMA version Unspecified (before 2008) LIMMA 3.26.8
LIMMA Software LIMMA package in Bioconductor GEO2R
Multiple test correction False discovery rate (FDR)
Adjusted p-value cut-off based on FDR 0.05