From: Quality assessment metrics for whole genome gene expression profiling of paraffin embedded samples
Mahoney et al. | Chow et al. |
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Normalize Data | Â |
Calculate Stress and dfArray | Calculate Outlier using un-normalized raw data |
(Plot Stress vs dfArray) | |
Stage 1: Remove arrays with Stress ≥ 1.5 | Stage 1: Remove arrays with Outlier ≥ Th*median(Outlier) (Default Th = 2) |
Renormalize data after removing bad arrays | Renormalize data after removing bad arrays |
Calculate dfArray on renormalized data | Calculate Outlier on renormalized data |
Stage 2: Investigate arrays with dfArray ≥ 2 | Stage 2: Remove arrays with Outlier ≥ Th*median(Outlier) (Default Th = 2) |
Final normalization after removing all outlying arrays | Â |