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