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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

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