Table 1.
Datasets used in this analysis
| GEO Accession Number | Reference | Data Format | Sample Number | Platform Type (probe number) |
|---|---|---|---|---|
| GSE7849 | Anders et al., 2008 [51] | Processed only | 78 | Affymetrix Human Genome U95 Version 2 Array (12,625 probes) |
| GSE3143 | Bild et al., 2006 [52] | Raw .CEL files | 158 | Affymetrix Human Genome U95 Version 2 Array (12,625 probes) |
| GSE12276 | Bos et al., 2009 [53] | Raw .CEL files | 204 | Affymetrix U133 Plus 2.0 (54,675 probes) |
| GSE22219 | Buffa et al., 2011 [44] | Raw Data files | 216 | Illumina humanRef-8 v1.0 expression beadchip |
| GSE10510 | Calabro et al., 2009 [54] | Raw .gpr files | 152 | DKFZ Division of Molecular Genome Analysis Human Operon 4.0 oligo Array 35 k (36,486 probes) |
| NA | Chang et al., 2005 [31] | Processed only | 295 | Agilent 21 K oligo array (22,575 probes) |
| NA | Chin et al., 2006 [55] | Processed only | 118 | Affymetrix U133AAofAv2 (22,944 probes) |
| GSE9893 | Chanrion et al., 2008 [56] | Raw data available | 155 | MLRG Human 21 K V12.0 (22,656 probes) |
| GSE7390 | Desmedt et al., 2007 [57] | Raw .CEL files | 198 | Affymetrix U133A (22,283 probes) |
| GSE16391 | Desmedt et al., 2009 [58] | Raw .CEL files | 48 | Affymetrix U133 Plus 2.0 (54,675 probes) |
| GSE25055 | Hatzis et al., 2011 [59] | Raw .CEL files | 508 | Affymetrix U133A (22,283 probes) |
| GSE24450 | Heikkinen et al., 2011 [60] | Raw Data files | 183 | Illumina HumanHT-12 V3.0 expression beadchip |
| GSE1992 | Hu et al., 2006 [27] | Processed only | 99 | Agilent 21 K oligo array (22,575 probes) |
| GSE20685 | Kao et al., 2011 [61] | Raw .CEL files | 327 | Affymetrix U133 Plus 2.0 (54,675 probes) |
| NA | Kok et al., 2009 [62] | Processed only | 109 | Agilent 44 K oligo array (54,675 probes) |
| GSE9195 | Loi et al., 2008 [63] | Raw .CEL files | 77 | Affymetrix U133 Plus 2.0 (54,675 probes) |
| GSE6532 | Loi et al., 2008 [63] | Raw .CEL files | 265 | Affymetrix U133A/B (22,283/22,645 probes) and U133 Plus 2.0 |
| GSE1378, GSE 1379 | Ma et al., 2004 [64] | Processed only | 60 | Custom 22 K oligo array (22,575 probes) |
| GSE3494 | Miller et al., 2005 [65] | Raw .CEL files | 251 | Affymetrix U133A/B (22,283/22,645 probes) |
| GSE45255 | Nagalla et l., 2013 [66] | Raw .CEL files | 139 | Affymetrix U133A (22,283 probes) |
| GSE1456 | Pawitan et l., 2005 [67] | Raw .CEL files | 159 | Affymetrix U133A/B (22,283/22,645 probes) |
| GSE21653 | Sabatier et al., 2010 [68] | Raw .CEL files | 266 | Affymetrix U133 Plus 2.0 (54,675 probes) |
| GSE11121 | Schmidt et al., 2008 [69] | Raw .CEL files | 200 | Affymetrix U133A (22,283 probes) |
| GSE17907 | Sircoulomb et al., 2010 [70] | Raw .CEL files | 51 | Affymetrix U133 Plus 2.0 (54,675 probes) |
| GSE2034 | Wang et al., 2006 [71] | Raw .CEL files | 286 | Affymetrix U133A (22,283 probes) |
| GSE12093 | Zhang et al., 2008 [72] | Raw .CEL files | 136 | Affymetrix U133A (22,283 probes) |
| Total | 4738 |