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Table 1 Quality assessment strategies for Formalin Fixed Paraffin-Embedded tissues analyzed with Illumina’s DASL assay

From: Quality assessment metrics for whole genome gene expression profiling of paraffin embedded samples

Mahoney et al. Chow et al.
Normalize Data  
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