Table 3.
Four replicates across seven microarray lots.
| Sample ID | Lot # | RAW Q | Background | SF | Present | GAPDH 3′/5′ | Actin 3′/5′ |
|---|---|---|---|---|---|---|---|
| PBR05_04 | 4018097 | 2.32 | Avg: 76.49, Stdev: 0.93, Max: 79.2, Min: 74.2 | 3.31 | 43.8% | 0.92 | 1.06 |
| PBR05_05 | 4018097 | 3.00 | Avg: 98.50, Stdev: 0.95, Max: 101.7, Min: 96.0 | 2.15 | 44.8% | 0.90 | 1.01 |
| PBR05_12 | 4018097 | 2.36 | Avg: 77.04, Stdev: 0.71, Max: 79.4, Min: 75.5 | 2.81 | 45.5% | 0.88 | 1.04 |
| PBR05_20 | 4018097 | 2.38 | Avg: 79.43, Stdev: 1.35, Max: 83.6, Min: 75.8 | 3.31 | 42.7% | 0.96 | 1.08 |
| PBR05_02 | 4018356 | 2.37 | Avg: 77.51, Stdev: 0.70, Max: 79.8, Min: 75.5 | 2.83 | 45.4% | 0.91 | 1.03 |
| PBR05_03 | 4018356 | 2.37 | Avg: 77.75, Stdev: 0.84, Max: 81.6, Min: 76.2 | 3.00 | 43.8% | 0.92 | 1.07 |
| PBR05_06 | 4018356 | 2.91 | Avg: 96.46, Stdev: 1.26, Max: 100.8, Min: 92.7 | 2.39 | 44.2% | 0.94 | 1.06 |
| PBR05_09 | 4018356 | 2.37 | Avg: 79.12, Stdev: 1.17, Max: 82.7, Min: 75.8 | 2.81 | 44.5% | 0.91 | 1.07 |
| PBR05_13 | 4025536 | 4.47 | Avg: 149.66, Stdev: 14.13, Max: 184.4, Min: 117.6 | 1.74 | 43.9% | 0.91 | 1.10 |
| PBR05_16 | 4025536 | 6.48 | Avg: 203.97, Stdev: 23.76, Max: 294.1, Min: 157.5 | 1.96 | 41.7% | 0.89 | 1.12 |
| PBR05_22 | 4025536 | 5.79 | Avg: 194.80, Stdev: 16.65, Max: 242.4, Min: 152.4 | 1.88 | 41.9% | 0.91 | 1.12 |
| PBR05_26 | 4025536 | 4.60 | Avg: 157.97, Stdev: 12.91, Max: 182.0, Min: 131.3 | 2.52 | 41.2% | 0.86 | 1.16 |
| PBR05_01 | 4028989 | 1.94 | Avg: 61.68, Stdev: 0.69, Max: 63.5, Min: 59.6 | 2.68 | 46.0% | 0.90 | 1.11 |
| PBR05_08 | 4028989 | 2.51 | Avg: 80.28, Stdev: 0.86, Max: 83.1, Min: 77.3 | 1.90 | 46.0% | 0.91 | 1.09 |
| PBR05_15 | 4028989 | 2.66 | Avg: 86.92, Stdev: 1.10, Max: 90.6, Min: 82.9 | 1.95 | 44.9% | 0.89 | 1.03 |
| PBR05_21 | 4028989 | 2.50 | Avg: 80.86, Stdev: 1.19, Max: 84.4, Min: 76.7 | 1.95 | 45.6% | 0.90 | 1.10 |
| PBR05_07 | 4028990 | 2.70 | Avg: 87.64, Stdev: 1.28, Max: 91.4, Min: 82.7 | 1.98 | 44.5% | 0.90 | 1.07 |
| PBR05_11 | 4028990 | 2.08 | Avg: 66.92, Stdev: 1.02, Max: 70.4, Min: 64.3 | 2.96 | 43.0% | 0.90 | 1.13 |
| PBR05_19 | 4028990 | 2.07 | Avg: 66.19, Stdev: 0.63, Max: 67.9, Min: 64.2 | 2.78 | 43.2% | 0.92 | 1.12 |
| PBR05_23 | 4028990 | 2.48 | Avg: 80.05, Stdev: 1.04, Max: 84.0, Min: 76.8 | 1.95 | 44.9% | 0.89 | 1.10 |
| PBR05_10 | 4029025 | 2.15 | Avg: 67.21, Stdev: 2.39, Max: 73.8, Min: 61.6 | 3.10 | 43.7% | 0.94 | 1.04 |
| PBR05_18 | 4029025 | 2.39 | Avg: 78.84, Stdev: 2.18, Max: 86.4, Min: 74.1 | 2.46 | 43.8% | 0.90 | 1.10 |
| PBR05_24 | 4029025 | 2.99 | Avg: 90.98, Stdev: 2.19, Max: 97.9, Min: 86.0 | 1.90 | 44.7% | 0.92 | 1.04 |
| PBR05_27 | 4029025 | 2.03 | Avg: 65.44, Stdev: 1.22, Max: 69.5, Min: 62.1 | 2.95 | 44.0% | 0.90 | 1.09 |
| PBR05_14 | 4029310 | 2.82 | Avg: 91.16, Stdev: 1.43, Max: 95.7, Min: 86.6 | 1.92 | 43.4% | 0.91 | 1.07 |
| PBR05_17 | 4029310 | 2.22 | Avg: 72.65, Stdev: 0.92, Max: 75.1, Min: 69.8 | 3.01 | 42.9% | 0.94 | 1.08 |
| PBR05_25 | 4029310 | 2.35 | Avg: 77.25, Stdev: 2.48, Max: 83.3, Min: 71.0 | 2.76 | 42.7% | 0.92 | 1.05 |
| PBR05_28 | 4029310 | 2.20 | Avg: 71.88, Stdev: 1.66, Max: 74.9, Min: 67.4 | 2.85 | 42.4% | 0.95 | 1.08 |
These findings were confirmed by two individual non-pooled samples, each run twice (Table 4). For more details on these QC parameters, please refer to Affymetrix notes on U133Plus2 microarrays.