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Table 1 Evaluation data sets

From: CGHpower: exploring sample size calculations for chromosomal copy number experiments

Data Set Array Type Probes Regions Cancer Type Groups (Samples)
Chin et al. spotted oligo 26,755 223 breast ER+ (113) vs. ER- (57)
Douglas et al. BAC 3,032 142 colorectal MSI (7) vs. CIN (30)
Fridlyand et al. BAC 1,877 231 breast TP53+ (10) vs. TP53- (52)
Myllykangas et al. cDNA 11,342 260 gastric diffuse (15) vs. intestinal (23)
Nymark et al. cDNA 10,953 242 lung asbestos-exposed (11) vs. non-exposed (9)
Postma et al. spotted oligo 26,755 111 colorectal good (16) vs. bad response (16)
Smeets et al. BAC 4,196 143 head and neck HPV+ (12) vs. HPV- (12)
Wrage et al. spotted oligo 25,549 23 lung BM+ (13) vs. BM- (15)
Simulation 0 in-situ oligo 42,331 440   (15) vs. (15)
Simulation 5 in-situ oligo 42,331 489   (15) vs. (15)
Simulation 10 in-situ oligo 42,331 525   (15) vs. (15)
  1. Eight public data sets were collected to evaluate the performance of CGHpower. They represented five different cancer types and BAC, cDNA and oligo-based microarray platforms, with resolutions varying from 2 K to 27 K array elements. The last column contains the distinguishing factor used to divide the data set into two groups, along with the number of arrays in each group. The simulated data sets were generated by introducing artificial aberrations into a set of clinical genetics samples. A total of 11 simulations were generated, and the remaining ones are available at http://www.cangem.org/cghpower/. ER = estrogen receptor, MSI = microsatellite instability, CIN = chromosomal instability, HPV = human papilloma virus, BM = bone marrow metastasis.