Table 1 Pre- and post-chip variables assessed in the current study on U133A arrays, with indications of the recommended acceptable range (where available) and summary statistics determined for samples in the current study. * None of the chips had significant spatial artifacts of hybridisation (e.g. scratches, uneven hybridisation) as assessed by visual inspection of the chip following hybridisation and by assessment of array and single outlier status across the chips. MAD is the median absolute deviation.
Variable | Variable (abbreviated) | Recommended acceptable range | Summary statistics (current experiment) | |||
|---|---|---|---|---|---|---|
| Â | Â | Â | Median | MAD | Range | |
Pre-chip variables | ||||||
Post mortem interval hours | PMI | empirical | 12 | 3 | 4 | 29 |
Subjective RNA quality 4 point scale | SUBQUAL | empirical | 3 | 1 | 1 | 4 |
RNA Integrity Number (RIN) 0 to 10 | RIN | empirical | 7.8 | 0.9 | 4.3 | 9.5 |
Adjusted cRNA yield (μg) | YIELD | >15 μg | 57 | 7 | 30 | 83 |
Post-chip variables: assessed within MAS 5.0 (Affymetrix) | ||||||
Background | BG | < 100 | 101.3 | 11.99 | 72.32 | 438.41 |
Noise (Raw Q) | RAWQ | 1.5 – 3.0 | 3.73 | 0.35 | 2.83 | 9.52 |
Noise | NOISE | empirical | 5.76 | 0.82 | 3.85 | 38.2 |
%P | PC_PRESENT | 25 – 50% | 47 | 2 | 24 | 53 |
Scaling Factor | SF | < 10 | 2.18 | 0.385 | 1.08 | 7.68 |
3'/5' ratio of β-Actin | B_ACTIN35 | < 3 | 1.6 | 0.26 | 0.98 | 55.87 |
3'/5' ratio of GAPDH | GAPDH35 | < 1.25 | 1.2 | 0.16 | 0.77 | 31.62 |
Post-chip variables: assessed within dChip [9] | ||||||
PM/MM difference array outlier algorithm* | DCHIP_AR_OUTLIER | < 5% | 0.37 | 0.2 | 0.04 | 47.59 |
PM/MM difference single outlier algorithm* | DCHIP_SING_OUTLIER | < 5% | 0.09 | 0.03 | 0.04 | 2.3 |
%P | DCHIP_PCCALL | 25 – 50% | 58.4 | 1.6 | 36.2 | 63.4 |
Median intensity | MEDINT | empirical | 358 | 43.5 | 231 | 1620 |
Post-chip variables: assessed within Affy, Bioconductor, developed by Collin, 2005 [13] | ||||||
Median NUSE | MED_NUSE | < 1.05 | 1.01 | 0.01 | 0.98 | 1.26 |
IQR.LR1 | IQR_LR1 | empirical | 0.23 | 0.03 | 0.15 | 1.04 |
B.LR1 | B_LR1 | empirical | 0.005 | 0.02 | -0.11 | 0.24 |
IQRplusAbsB.LR1 | IQRplusAbsB_LR1 | empirical | 0.24 | 0.04 | 0.15 | 1.13 |
CV.LR1 | CV_LR1 | empirical | 6.41 | 3.9 | 0.01 | 35.91 |
IQR.LR2 | IQR_LR2 | empirical | 0.18 | 0.03 | 0.11 | 0.98 |
B.LR2 | B_LR2 | empirical | 0 | 0.01 | -0.1 | 0.22 |
IQRplusAbsB.LR2 | IQRplusAbsB_LR2 | empirical | 0.2 | 0.035 | 0.12 | 1.02 |
CV.LR2 | CV_LR2 | empirical | 3.97 | 3.225 | 0 | 33.8 |
Post-chip variables: assessed within Affy, Bioconductor [13] | ||||||
RNA degradation plot (gradient) | RNADEG_SLOPE | empirical | 2.27 | 0.27 | 0.86 | 3.96 |
RNA degradation plot (P- value from the linear regression) | PVAL_SLOPE | empirical | 2.67E-08 | 2.60e-8 | 4.21e-12 | 0.0049 |