Table 4.

Survival breast cancer data sets with the OS and RFS endpoints

Data set	Platform	Pre-normalization	Gene nb	Sample size	Ref.	Treatment	Survival outcome
GSE3143	Affymetrix, HG-U95A	MAS5.0	8660	158	Bild 06 [ 56 ]	Unknown	OS
GSE1456A&B	Affymetrix, HG-U133A&B	MAS5.0, global mean	15848	159	Pawitan 05 [ 57 ]	Adj. Chemotherapy (incl. Tamoxifen)	OS, RFS
GSE4335	cDNA	Scaling	12793	122	Sorlie 03 [ 54 ]	Neoadj. Chemo/chemo (Tamoxifen)-82 patients	OS, RFS
GSE1992	Agilent	LOWESS	15528	170	Hu 06 [ 22 ]	Treated	OS, RFS
Vijver	Agilent	Scaling	13628	295	Van de Vijver 02 [ 55 ]	Chemo/hormonal therapy (90 patients)	OS, RFS
GSE2990	Affymetrix, HG-U133A	RMA	12010	189	Sotiriou 06 [ 58 ]	Tamoxifen (64 patients)	RFS
GSE2034	Affymetrix, HG-U133A	MAS5.0	12010	286	Wang 05 [ 59 ]	None	RFS
GSE4922A&B	Affymetrix, HG-U133A&B	MAS5.0, global mean	15848	289	Ivshina 06 [ 60 ]	Systemic/endocrine therapy (147 vs. 66 patients)	RFS
Merged OS	Affymetrix, Agilent, cDNA		7049	849			OS
Merged RFS	Affymetrix, Agilent, cDNA		9181	1324			RFS

Gene nb refers to the number of genes. MAS 5.0 refers to Affymetrix Microarray Suite version 5.0 and LOWESS stands for LOcally WEighted Scatterplot Smoothing and RMA for Robust Microarray Analysis, respectively. Adj. stands for adjuvant and chemo for chemotherapy. Merged OS refers to merged data sets with OS endpoint and Merged RFS refers to the merged data sets with RFS endpoint. The expression values of dual channel data were already ${\log }_2$ -transformed. Among the data sets generated by Affymetrix, the absolute intensity values of GSE3143, GSE2034 and GSE2990 were ${\log }_2$ -transformed for this study as the rest of Affymetrix data sets were already ${\log }_2$ -transformed by the authors.