Table 1.
Pre-processing strategies assessed in this study
| Name | Bg correction | Transformation | Normalization |
|---|---|---|---|
| logq | None | Log2 | Quantile |
| vstq | Vst (implicit) | Vst | Quantile |
| vstr | Vst (implicit) | Vst | Robust spline |
| neq | Normexp (mle) | Log2 | Quantile |
| neqc | Normexp | Log2 | Quantile |
| (using negative controls) | (including controls) |
For logq, neq and neqc, background correction is performed first, then between-array normalization, then transformation. For vstq and vstr, transformation is performed first followed by between-array normalization.