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Table 2 Reproducibility of replicate hybridisations and signal response to copy number

From: Evaluation of high-resolution microarray platforms for genomic profiling of bone tumours

Platform Corr TC-32 Corr OSA 0n: CDKN2A
TC-32
1n: 9p21.3-p21.2
TC-32
Log2ratio (SD)
2n: Chr 2
TC-32
Log2ratio (SD)
3n: Chr 8
TC-32
Log2ratio (SD)
4n: 1q
TC-32
Log2ratio (SD)
>10n: MDM2
OSA
    Log2ratio (SD) Size [kb]      Log2ratio (SD) Size [kb]
Theoretical value 1.0 1.0 < -3 - -1.0 0.0 0.58 1.0 > 3 -
Affymetrix Genome-Wide Human SNP Array 6.0 0.75 0.84 -1.79 (0.93) 166 -0.53 (0.43) 0.00 (0.41) 0.34 (0.44) 0.56 (0.44) 1.86 (0.49) 146
    -2.09 (0.92) 148 -0.62 (0.35) 0.00 (0.32) 0.37 (0.34) 0.59 (0.34) 1.99 (0.50) 146
Agilent Human Genome CGH 244A 0.91 0.91 -4.72 (1.57) 135 -0.96 (0.31) 0.00 (0.19) 0.52 (0.27) 0.92 (0.22) 4.69 (0.24) 147
    -4.83 (1.53) 135 -0.97 (0.30) 0.01 (0.21) 0.54 (0.29) 0.95 (0.25) 4.74 (0.21) 147
Illumina HumanExon510 s-duo 0.96 0.94 -4.72 (1.07) 171 -0.67 (0.54) -0.05 (0.20) 0.22 (0.29) 0.36 (0.26) 1.24 (0.59) 122
    -4.69 (0.91) 171 -0.67 (0.59) -0.05 (0.20) 0.22 (0.29) 0.36 (0.26) 1.23 (0.58) 122
Nimblegen HG18 CGH 385 k WG Tiling v1.0 0.63 0.73 -0.85 (0.57) 169 -0.45 (0.30) -0.06 (0.19) 0.24 (0.21) 0.48 (0.24) 2.58 (0.98) 156
    -0.88 (0.50) 169 -0.47 (0.29) -0.06 (0.20) 0.26 (0.21) 0.53 (0.23) 2.46 (1.0) 156
  1. Pearson's correlation of log2 ratios for the replicate hybridisations based on all data points and the average log2 ratio with standard deviation for six specific chromosomes or chromosomal regions, representing 0, 1, 2, 3 and 4 copies in TC-32, as well as high-level amplification in OSA, for each hybridisation. In addition, the measured size of the regions for homozygous deletion of the CDKN2A locus in TC-32 and high-level amplification of the MDM2 locus in OSA is given for each hybridisation.