Microarray Normalization Revisited for Reproducible Breast Cancer Biomarkers

Table 1

Studies in GEO used for present work.

Idx	GSE-ID	City	No. of samples used	Samples in GEO	Criteria for excluding samples					Sample-ID	PMID	Public on
					Controls	Duplicates	Replicates	Others	Comment to excluded others
1	GSE31448	Marseille	347	357	4			6	Did not pass quality control	1611-1963	22110708	Dec 02, 2011
2	GSE20685	Taipei	327	327						757-1083	21501481	Apr 24, 2011
3	GSE26639	Paris Cedex 05	226	226						1331-1556	22110708	Jun 08, 2011
4	GSE12276	Rotterdam	203	204		1				117-319	19421193	Jun 13, 2009
5	GSE76124	Houston	198	198						3301-3498	25208879; 26921331	Dec 18, 2015
6	GSE65194	Paris	153	178	11			14	Cell line	2934-3086	25848952; 23700430; 23144294	Jan 23, 2015
7	GSE71258	Missouri	128	128						3173-3300	26269605	Dec 16, 2015
8	GSE16446	Toronto	120	120						426-545	21422418; 20098429; 20189874	Jan 26, 2010
9	GSE88770	Brussels	116	117		1				1215-1330	23028037	Oct 15, 2016
10	GSE23177	Leuven	116	116						3597-3712	21116709	Feb 04, 2011
11	GSE19615	Manhattan	115	115						642-756	20098429	Jan 05, 2010
12	GSE43365	Boston	111	111						2260-2370	na	Jun 03, 2013
13	GSE36771	Auckland	107	107						1992-2098	22564725	Mar 31, 2012
14	GSE58812	Saint Herblain	107	107						2675-2781	25887482	May 19, 2015
15	GSE42568	Dublin	102	121	17			2	Did not pass quality control	2099-2202	23740839	May 26, 2013
16	GSE58984	Brussels	94	94						2782-2875	na	Dec 31, 2016
17	GSE20711	Toronto	88	90	2					1084-1171	21910250	Oct 19, 2011
18	GSE6532	Toronto	87	741				654	Other than breast cancer tissue	30-116	17401012; 18498629; 20479250	Mar 01, 2007
19	GSE66305	Modena	86	88				2	Did not pass quality control	3087-3172	26245675	Oct 06, 2015
20	GSE48390	New Taipei City	81	81						2466-2546	24098497	Jan 07, 2014
21	GSE18864	Lyngby	75	84			9			567-641	20100965; 20098429; 20189874	Nov 04, 2009
22	GSE76274	Houston	67	67						3499-3565	25208879; 26921331	Dec 23, 2015
23	GSE61304	Singapore	58	62	4					2876-2933	26517092; 26474389	May 10, 2015
24	GSE43358	Brussels	57	57						2203-2259	25412710	Nov 21, 2014
25	GSE95700	Taipei City	57	57						3713-3769	28299476	Jun 13, 2017
26	GSE16391	Toronto	55	55						371-425	19573224	Jul 09, 2009
27	GSE29431	Barcelona	46	66	12			8	Did not pass quality control	1557-1610	na	Dec 22, 2011
28	GSE12777	South San Francisco	51	51						320-370	19567590; 21673316	Jan 12, 2009
29	GSE58792	New York	51	51						2624-2674	25190728	Jul 01, 2014
30	GSE46222	Washington	48	49				1	CEL not processable in R	2371-2418	na	Apr 15, 2015
31	GSE47389	Rotterdam	47	47						2419-2465	23993096	Nov 01, 2013
32	GSE22035	Saint-Cloud	43	43						1172-1214	21209903	Jan 10, 2011
33	GSE48905	Hørsholm	42	42						2547-2588	24505287	Jan 08, 2014
34	GSE50567	Gliwice	35	41	6					2589-2623	21196292	Sep 05, 2013
35	GSE87007	Brussels	31	31						3566-3596	28566333	Jan 01, 2017
36	GSE5460	Boston	29	129		98		2	CELs not processable in R	1-29	18297396	May 26, 2007
37	GSE27120	Brussels	28	79	3			48	No receptor status	1964-1991	22235100	Mar 15, 2012
38	GSE18728	Seattle	21	61			40			546-566	20012355	Oct 30, 2009
Total:			3753	4698	59	100	49	737