Table 1.
Seven pairs (fourteen in total) of independent microarray datasets used for benchmarking
| Phenotype | Dataset name and reference | Class 1 (control group) samples | Class 2 (case group) samples | Data source | Platform |
|---|---|---|---|---|---|
| Effect of smoking on bronchial epithelium | Never smokers | Current smokers | |||
| Beane [18] | 21 | 52 | GSE7895 | U133A | |
| Vanni [19] | 22 | 37 | GSE10135 | U133 Plus 2 | |
| Subtypes of non-small cell lung cancer (NSCLC) | AD (adenocarcinoma) | SCC (squamous cell carcinoma) | |||
| Bild [20] | 58 | 53 | GSE3141 | U133 Plus 2 | |
| Lee [21] | 63 | 75 | GSE8894 | U133 Plus 2 | |
| Subtypes of primary high grade glioma | AA (anaplastic astrocytoma) | GBM (glioblastoma multiforme) | |||
| Phillips [22] | 21 | 56 | GSE4271 | U133 Set | |
| Sun [23] | 19 | 77 | GSE4290 | U133 Plus 2 | |
| Estrogen receptor (ER) status in breast cancer | ER-negative | ER-positive | |||
| Chin [24] | 46 | 84 | E-TABM-158 | U133A | |
| Minn [25] | 42 | 57 | GSE2603 | U133A | |
| Breast cancer grade | Grade 1 | Grade 3 | |||
| Desmedt [26] | 30 | 83 | GSE7390 | U133A | |
| Sotiriou [27] | 28 | 32 | GSE2990 | U133A | |
| Lung cancer grade | Grade 1 | Grade 3 | |||
| Dana-Farber [28] | 13 | 37 | Author's website | U133A | |
| Michigan [28] | 26 | 66 | |||
| Clear cell renal cell carcinoma (CCRCC) vs Normal kidney | Normal kidney | Tumorous kidney | |||
| Jones [29] | 23 | 32 | GSE15641 | U133A | |
| Kort [30] | 12 | 10 | GSE11024 | U133 Plus 2 | |
Each of the datasets was referred to in the main text by the dataset name, which is the first author's name or cohort name. Numbers in the table indicate the number of samples.