. 2006 Sep 7;1:27. doi: 10.1186/1745-6150-1-27

Table 4.

Summary of values of the coefficients of standard deviation function and K_αcoefficients

GeneChip/average/SD/CV	No. of probe sets	Cons. samp. size	No. of arrays	No. of comp.	Coefficient. of st. dev. function		Average Kalpha values in given probability intervals

					a1	a2	0.500	0.600	0.700	0.800	0.900	0.950	0.990	0.995
*Total average [sum]*			*[682]*	*[900]*	*9.66*	*0.266*	*0.642*	*0.808*	*1.009*	*1.275*	*1.711*	*2.145*	*3.226*	*3.741*
*Total SD*					*9.99*	*0.146*	*0.033*	*0.039*	*0.043*	*0.045*	*0.052*	*0.080*	*0.270*	*0.390*
*Total CV*					*1.03*	*0.550*	*0.052*	*0.049*	*0.043*	*0.035*	*0.030*	*0.037*	*0.084*	*0.104*

HuGeneFL [a1]	7070	12	11	54	8.61	0.115	0.64	0.81	1.01	1.27	1.71	2.16	3.41	4.09
HuGeneFL [b]	7070	12	13	78	8.09	0.418	0.61	0.77	0.97	1.24	1.73	2.24	3.58	4.18
HuGeneFL [c]	7070	25	5	10	34.58	0.435	0.61	0.76	0.94	1.20	1.60	2.03	3.39	4.10
HuGeneFL [c]	7070	25	5	10	28.93	0.393	0.59	0.73	0.92	1.18	1.60	2.07	3.42	4.07

*HuGeneFL avg [sum]*			*[34]*	*[152]*	*20.05*	*0.34*	*0.61*	*0.77*	*0.96*	*1.22*	*1.66*	*2.13*	*3.45*	*4.11*
*HuGeneFL SD*					*13.71*	*0.15*	*0.02*	*0.03*	*0.04*	*0.04*	*0.07*	*0.10*	*0.09*	*0.05*
*HuGeneFL CV*					*0.68*	*0.44*	*0.04*	*0.04*	*0.04*	*0.04*	*0.04*	*0.05*	*0.03*	*0.01*

HG-U95Av2 [d]	12559	12	5	10	6.30	0.688	0.61	0.78	1.00	1.30	1.83	2.32	2.98	3.26
HG-U95Av2 [e1]	12559	25	15	15	10.49	0.199	0.65	0.82	1.01	1.27	1.68	2.07	3.05	3.55
HG-U95Av2 [e2]	12559	25	15	15	10.59	0.200	0.64	0.81	1.01	1.26	1.67	2.07	3.07	3.56
HG-U95Av2 [e3]	12559	25	15	15	10.41	0.189	0.63	0.80	1.00	1.25	1.66	2.07	3.06	3.55
HG-U95Av2 [e4]	12559	25	12	12	10.91	0.185	0.63	0.79	0.99	1.24	1.66	2.04	3.02	3.50
HG-U95Av2 [e5]	12559	25	4	2	6.50	0.394	0.65	0.82	1.01	1.26	1.65	2.05	3.05	3.62
HG-U95Av2 [f]	12559	25	4	2	5.64	0.155	0.64	0.81	1.00	1.25	1.66	2.04	2.92	3.31
HG-U95Av2 [g1]	12559	25	2	1	4.79	0.479	0.61	0.76	0.95	1.20	1.64	2.10	3.22	3.71
HG-U95Av2 [g1]	12559	25	5	10	3.31	0.500	0.64	0.80	1.00	1.26	1.69	2.09	2.98	3.29

*HG-U95Av2 avg [sum]*			*[77]*	*[82]*	*7.66*	*0.33*	*0.63*	*0.80*	*1.00*	*1.26*	*1.68*	*2.09*	*3.04*	*3.48*
*HG-U95Av2 SD*					*2.94*	*0.19*	*0.02*	*0.02*	*0.02*	*0.03*	*0.06*	*0.09*	*0.08*	*0.16*
*HG-U95Av2 CV*					*0.38*	*0.57*	*0.02*	*0.02*	*0.02*	*0.02*	*0.04*	*0.04*	*0.03*	*0.05*

HG-U95B [d]	12563	12	5	10	16.26	0.636	0.63	0.80	1.01	1.30	1.80	2.28	3.18	3.68
HG-U95B [e5]	12563	25	2	1	17.95	0.167	0.64	0.80	0.99	1.24	1.65	2.02	3.08	3.54
HG-U95C [d]	12587	12	5	10	20.57	0.603	0.64	0.81	1.02	1.30	1.77	2.25	3.39	3.98
HG-U95C [e5]	12587	25	2	1	16.42	0.178	0.63	0.79	0.99	1.23	1.62	2.00	3.06	3.61
HG-U95D [d]	12587	12	5	10	39.79	0.501	0.62	0.78	0.99	1.28	1.77	2.33	3.80	4.42
HG-U95D [e5]	12587	25	2	1	54.45	0.240	0.63	0.79	0.99	1.23	1.62	2.05	2.98	3.48
HG-U95E [d]	12582	12	5	10	31.84	0.534	0.60	0.76	0.97	1.27	1.78	2.29	3.53	4.08
HG-U95E [e5]	12582	25	2	1	45.64	0.215	0.63	0.79	1.00	1.25	1.64	2.02	2.88	3.31

*HG-U95B to E avg [sum]*			*[28]*	*[44]*	*30.37*	*0.38*	*0.63*	*0.79*	*0.99*	*1.26*	*1.71*	*2.16*	*3.24*	*3.76*
*HG-U95B to E SD*					*14.87*	*0.20*	*0.01*	*0.01*	*0.02*	*0.03*	*0.08*	*0.14*	*0.31*	*0.37*
*HG-U95B to E CV*					*0.49*	*0.53*	*0.02*	*0.02*	*0.02*	*0.02*	*0.05*	*0.07*	*0.10*	*0.10*

HG-U133A 2.0 [e6]	22225	25	15	15	4.55	0.091	0.65	0.82	1.02	1.28	1.72	2.14	3.14	3.62
HG-U133A 2.0 [e7]	22225	25	15	15	4.50	0.106	0.66	0.84	1.04	1.31	1.75	2.17	3.18	3.63
HG-U133A 2.0 [e8]	22225	25	12	12	4.10	0.108	0.67	0.84	1.05	1.32	1.77	2.21	3.26	3.75
HG-U133A 2.0 [h1]	22225	25	8	4	3.91	0.288	0.64	0.80	1.00	1.26	1.67	2.08	3.05	3.54
HG-U133A 2.0 [i1]	22225	12	4	6	6.25	0.210	0.65	0.82	1.01	1.27	1.68	2.08	3.04	3.48
HG-U133A 2.0 [j]	22225	25	5	10	6.54	0.390	0.62	0.79	0.98	1.25	1.68	2.10	3.13	3.62
HG-U133A 2.0 [j]	22225	25	5	10	5.54	0.393	0.62	0.79	0.98	1.25	1.66	2.08	3.10	3.64
HG-U133A 2.0 [k1]	22225	25	6	15	3.68	0.672	0.63	0.80	1.00	1.27	1.71	2.11	2.84	3.16
HG-U133A 2.0 [k1]	22225	25	3	3	4.95	0.435	0.59	0.74	0.93	1.19	1.65	2.15	3.37	3.79
HG-U133A 2.0 [l1]	22225	25	6	3	6.45	0.151	0.64	0.81	1.01	1.27	1.68	2.08	3.06	3.55
HG-U133A 2.0 [l2]	22225	25	12	6	6.78	0.148	0.65	0.82	1.02	1.27	1.67	2.06	2.93	3.33

*HG-U133A 2.0 avg [sum]*			*[91]*	*[99]*	*5.21*	*0.27*	*0.64*	*0.80*	*1.00*	*1.27*	*1.69*	*2.11*	*3.10*	*3.56*
*HG-U133A 2.0 SD*					*1.15*	*0.18*	*0.02*	*0.03*	*0.03*	*0.03*	*0.04*	*0.05*	*0.15*	*0.18*
*HG-U133A 2.0 CV*					*0.22*	*0.67*	*0.03*	*0.03*	*0.03*	*0.03*	*0.02*	*0.02*	*0.05*	*0.05*

HG-U133 Plus 2 [i2]	54000	50	8	10	3.94	0.188	0.68	0.85	1.06	1.33	1.76	2.17	3.11	3.55
HG-U133 Plus 2 [l3]	54000	50	20	27	4.03	0.086	0.65	0.82	1.02	1.28	1.69	2.07	2.95	3.34

*HG-U133 Plus 2 avg [sum]*			*[28]*	*[37]*	*3.99*	*0.14*	*0.67*	*0.83*	*1.04*	*1.30*	*1.72*	*2.12*	*3.03*	*3.44*

HG-Focus [k2]	8756	12	9	36	4.13	0.216	0.70	0.87	1.08	1.35	1.76	2.15	3.06	3.47
HG-Focus [k2]	8756	12	4	6	4.13	0.181	0.68	0.86	1.07	1.33	1.76	2.18	3.08	3.56
HG-Focus [k2]	8756	12	4	6	3.90	0.198	0.70	0.87	1.08	1.36	1.81	2.22	3.15	3.55
HG-Focus [k2]	8756	12	4	6	3.69	0.176	0.68	0.86	1.07	1.35	1.79	2.19	3.17	3.64
HG-Focus [k2]	8756	12	5	10	3.46	0.183	0.67	0.85	1.05	1.33	1.77	2.19	3.12	3.49
HG-Focus [k2]	8756	12	4	6	4.01	0.205	0.71	0.89	1.10	1.38	1.81	2.19	3.11	3.53
HG-Focus [k2]	8756	12	4	6	3.98	0.174	0.68	0.85	1.06	1.32	1.74	2.14	3.06	3.43

*HG-Focus avg [sum]*			*[34]*	*[76]*	*3.90*	*0.19*	*0.69*	*0.86*	*1.07*	*1.35*	*1.78*	*2.18*	*3.11*	*3.52*
*HG-Focus SD*					*0.24*	*0.02*	*0.01*	*0.02*	*0.02*	*0.02*	*0.03*	*0.03*	*0.04*	*0.07*
*HG-Focus CV*					*0.06*	*0.08*	*0.02*	*0.02*	*0.01*	*0.01*	*0.01*	*0.01*	*0.01*	*0.02*

MG-Mu11kSubA, SubB [a]	13069	12	10	20	9.98	0.121	0.59	0.75	0.95	1.22	1.70	2.20	3.65	4.48
MG-Mu11kSubA, SubB [a]	13069	12	10	20	8.03	0.170	0.59	0.74	0.94	1.20	1.68	2.19	3.78	4.66
MG-Mu11kSubA, SubB [a]	13069	12	10	20	8.21	0.145	0.60	0.76	0.96	1.23	1.70	2.21	3.70	4.52
MG-Mu11kSubA, SubB [a]	13069	12	10	20	5.32	0.139	0.56	0.71	0.91	1.19	1.71	2.30	4.03	4.84
MG-Mu11kSubA, SubB [m1]	13069	12	8	4	13.86	0.321	0.64	0.81	1.01	1.28	1.73	2.22	3.62	4.24
MG Mu11kSubA, SubB [n1]	13069	12	20	10	11.84	0.420	0.66	0.82	1.01	1.26	1.71	2.21	3.61	4.32

*MG-Mu11kSubA, SubB avg [sum]*			*[68]*	*[94]*	*9.54*	*0.219*	*0.61*	*0.77*	*0.96*	*1.23*	*1.70*	*2.22*	*3.73*	*4.51*
*MG-Mu11kSubA, SubB SD*					*3.03*	*0.122*	*0.04*	*0.04*	*0.04*	*0.04*	*0.02*	*0.04*	*0.16*	*0.22*
*MG-Mu11kSubA, SubB CV*					*0.32*	*0.557*	*0.06*	*0.05*	*0.04*	*0.03*	*0.01*	*0.02*	*0.04*	*0.05*

Mu19kSubA, B, C [m2]	12420	12	12	6	15.41	0.314	0.63	0.79	0.99	1.25	1.73	2.26	3.95	4.56

MG-U74Av2 [o]	12588	12	6	6	8.72	0.180	0.59	0.75	0.95	1.23	1.70	2.20	3.56	4.30
MG-U74Av2 [o]	12588	12	5	4	6.97	0.230	0.58	0.74	0.94	1.23	1.71	2.24	3.68	4.48
MG-U74Av2 [p]	12588	12	7	21	9.50	0.125	0.59	0.75	0.95	1.24	1.72	2.21	3.54	4.30
MG-U74Av2 [q]	12588	12	5	4	4.97	0.229	0.68	0.85	1.06	1.33	1.76	2.19	3.23	3.76
MG-U74Av2 [l4]	12588	12	9	9	7.50	0.111	0.67	0.83	1.03	1.30	1.73	2.13	3.09	3.53
MG-U74Av2 [r]	12588	12	10	20	4.69	0.269	0.65	0.82	1.02	1.29	1.73	2.17	3.31	3.89
MG-U74Av2 [r]	12588	12	3	3	3.30	0.238	0.64	0.80	1.00	1.27	1.71	2.17	3.48	4.04
MG-U74Av2 [e5]	12588	12	2	1	3.83	0.184	0.64	0.81	1.00	1.27	1.69	2.10	3.15	3.80
MG-U74Av2 [g2]	12588	12	2	1	13.50	0.451	0.64	0.81	1.01	1.27	1.72	2.16	3.36	3.95
MG U74Av2 [n2]	12400	12	26	13	6.56	0.113	0.64	0.80	1.00	1.27	1.70	2.12	3.15	3.67

*MG-U74Av2 avg [sum]*			*[75]*	*[82]*	*6.96*	*0.213*	*0.63*	*0.80*	*1.00*	*1.27*	*1.72*	*2.17*	*3.36*	*3.97*
*MG-U74Av2 SD*					*3.07*	*0.101*	*0.03*	*0.04*	*0.04*	*0.03*	*0.02*	*0.04*	*0.20*	*0.31*
*MG-U74Av2 CV*					*0.44*	*0.472*	*0.06*	*0.05*	*0.04*	*0.02*	*0.01*	*0.02*	*0.06*	*0.08*

MG-U430A [l5]	22636	25	10	5	7.68	0.132	0.65	0.81	1.01	1.27	1.68	2.06	2.94	3.36
MG-U430A [l6]	22636	25	5	10	10.08	0.265	0.67	0.84	1.04	1.30	1.71	2.10	2.98	3.35
MG-U430A [l6]	22636	25	5	10	9.44	0.160	0.65	0.81	1.01	1.27	1.67	2.05	2.93	3.30

*MG-U430A*			*[20]*	*[25]*	*9.07*	*0.186*	*0.65*	*0.82*	*1.02*	*1.28*	*1.69*	*2.07*	*2.95*	*3.34*
*MG-U430A*					*1.24*	*0.070*	*0.01*	*0.02*	*0.02*	*0.02*	*0.02*	*0.03*	*0.03*	*0.03*
*MG-U430A*					*0.14*	*0.377*	*0.02*	*0.02*	*0.02*	*0.02*	*0.01*	*0.01*	*0.01*	*0.01*

RG-U34A [h2]	8740	12	35	34	1.82	0.316	0.64	0.81	1.01	1.28	1.73	2.21	3.40	3.95
RG-U34A [l7]	8740	12	6	3	3.25	0.226	0.68	0.85	1.06	1.33	1.76	2.17	3.20	3.77
RG-U34A, [l8]	8740	12	4	2	6.01	0.146	0.65	0.83	1.03	1.29	1.72	2.11	3.10	3.60

*RG-U34A avg [sum]*			*[45]*	*[39]*	*3.70*	*0.229*	*0.66*	*0.83*	*1.03*	*1.30*	*1.74*	*2.16*	*3.24*	*3.78*
*RG-U34A SD*					*2.13*	*0.085*	*0.02*	*0.02*	*0.02*	*0.02*	*0.02*	*0.05*	*0.15*	*0.17*
*RG-U34A CV*					*0.58*	*0.371*	*0.03*	*0.03*	*0.02*	*0.02*	*0.01*	*0.02*	*0.05*	*0.05*

*RT-U34 Neurobiology [l7]*	*982*	12	40	20	*1.77*	*0.194*	*0.60*	*0.75*	*0.96*	*1.22*	*1.65*	*2.08*	*3.12*	*3.38*

*Drosophila [s]*	*13976*	12	6	6	*2.20*	*0.081*	*0.66*	*0.83*	*1.04*	*1.31*	*1.73*	*2.17*	*3.21*	*3.67*

E. coli [t]	7290	12	38	39	3.09	0.337	0.65	0.83	1.04	1.32	1.78	2.24	3.45	4.03
E. coli [u]	7290	12	15	30	1.88	0.302	0.65	0.83	1.04	1.34	1.81	2.29	3.47	4.04

*E. Coli avg [sum]*			*[53]*	*[69]*	*2.23*	*0.228*	*0.64*	*0.81*	*1.02*	*1.30*	*1.74*	*2.19*	*3.31*	*3.78*

ATH1 [v1]	22700	25	14	17	9.22	0.307	0.68	0.85	1.05	1.31	1.71	2.09	2.95	3.31
ATH1 [v1]	22700	25	34	36	11.18	0.269	0.68	0.85	1.05	1.31	1.71	2.08	2.91	3.26
ATH1 [w]	22700	25	8	4	6.26	0.279	0.65	0.81	1.01	1.27	1.69	2.10	3.06	3.45
ATH1 [x]	22700	25	4	2	3.09	0.232	0.68	0.85	1.05	1.31	1.72	2.12	3.17	3.70
ATH1 [y]	22700	25	4	2	3.07	0.247	0.66	0.82	1.02	1.28	1.68	2.08	3.09	3.60

*ATH1 avg [sum]*			*[64]*	*[61]*	*6.57*	*0.267*	*0.67*	*0.84*	*1.04*	*1.30*	*1.70*	*2.09*	*3.03*	*3.46*
*ATH1 SD*					*3.63*	*0.029*	*0.01*	*0.02*	*0.02*	*0.02*	*0.02*	*0.02*	*0.11*	*0.19*
*ATH1 CV*					*0.55*	*0.108*	*0.02*	*0.02*	*0.02*	*0.02*	*0.01*	*0.01*	*0.03*	*0.05*

Arabidopsis [v2]	8200	12	7	8	7.69	0.403	0.75	0.94	1.14	1.40	1.79	2.15	2.89	3.18

No. of probe sets is approximate number of the probe sets on array, Cons. samp. size is number of the probe pairs in a consecutive sample, No. of arrays is a number of arrays tested, No. of comp. is the number of pair-wise comparisons among the replicates, coefficients a₁and a₂are the coefficients of standard deviation function and Kalpha is the coefficient determining probability interval; "h." stands for "human," "m." for "murine." Average values, sum of arrays and comparisons (in square brackets), standard deviations (SD) and coefficients of variation (CV) of each GeneChip type are printed in bold italics.

Data sources:

a1 – J. P. Novak et al., HuGeneFl, IMR90 human cell line [10].

a2 – J. P. Novak et al., HuGeneFl, mouse tissues, adult male C57BL/6 [10].

b – A.-M. Mes-Masson, P. Tonin and coworkers, HuGeneFL, normal ovarian surface epithelial (NOSE) primary cell cultures, private communication.

c – P. Permana, HuGeneFL, human skeletal muscle tissue [35].

d – P. Tonin and A.-M. Mes-Masson and coworkers, HG-U95A to E, epithelial ovarian cancer (EOC) cell line [36].

e1 – Affymetrix, HG-U95A, latin square, experiments 1 to 5.

e2 – Affymetrix, HG-U95A, latin square, experiments 6 to 10.

e3 – Affymetrix, HG-U95A, latin square experiments 11 to 15.

e4 – Affymetrix, HG-U95A, latin square, experiments 16 to 19.

e5 – Affymetrix, HG-U95A to E, Demo Data.

e6 – Affymetrix, HG-U133A, latin square, experiments 1 to 5.

e7 – Affymetrix, HG-U133A, latin square, experiments 6 to 10.

e8 – Affymetrix, HG-U133A, latin square, experiments 11 to 14.

f – M. S. Rolph, HG-U95Av2, primary human bronchial epithelial cells.

g1 – Z. Gatalica, HG-U95Av2, breast tumor tissues and normal breast tissue samples [37].

g2 – Z. Gatalica, MG-U74Av2, mouse kidney tissue.

h1 – M. Boerma, HG-U133A 2.0, primary human umbilical vein endothelial cells (HUVECs) and the immortalized HUVEC cell line EA.hy926 [38].

h2 – M. Boerma, RG-U34A, cultures enriched for neonatal rat cardiac myocytes or fibroblasts [39].

i1 – M. Hajduch, HG-U133A 2.0.

i2 – M. Hajduch, HG-U133 plus 2.

j – S. Y. Kim and D. J. Volsky, HG-U133A 2.0, human fetal astrocytes, normal and pseudotyped HIV-1 infected [40].

k1 – O. Modlich, HG-U133A 2.0, human superficial and invasive bladder tumors [41].

k2 – O. Modlich and Raschke, Focus arrays, human lymphoma cell line Kaspas-422, DSMZ no.: ACC 32 (follicular B cell).

l1 – C. Wang and J. Xu, HG-U133A 2.0, human lymphoblast cell line.

l2 – C. Wang and J. Xu, HG-U133A 2.0, human pancreatic islet.

l3 – C. Wang and J. Xu, HG-U133 Plus 2, Stratagene Universal Human Reference RNA, Ambion Human Brain Reference RNA and mixtures of both in different concentrations.

l4 – C. Wang and J. Xu, MG-U74Av2, mouse biliary epithelial cells.

l5 – C. Wang and J. Xu, MG-U430A, mouse spleen.

l6 – C. Wang and J. Xu, MG-U430A, myofibroblast cell line.

l7 – C. Wang and J. Xu, RG-U34A, rat livers.

l8 – C. Wang and J. Xu, RG-U34A, rat bone marrow stem cells.

m1 – McInnes and coworkers, MG-Mu11kSubA, SubB, retinal RNA samples from WT and Rom1 knock-out mice [36].

m2 – McInnes, Szego and coworkers, MG-Mu19kSubA, SubB, SubC, retinal RNA samples from WT and Rom1 knock-out mice [42].

n1 – Burton, McGehee and coworkers, MG-Mu11kSubA, SubB, 3T3-L1 adipocytes [43].

n2 – Burton, McGehee and coworkers, MG-U74Av2,3T3-L1 adipocyte cultures [44].

o – M. Cosio, MG-U74Av2, lung tissues, murine strains NZW and AKR.

p – R. St-Arnaud, MG-U74Av2, C2C12 cells [45].

q – J. Hidalgo, MG-U74Av2, cortex samples, C57B6 normal and IL6 KO mice [46].

r – D. Radzioch, C. Guilbault and coworkers, MG-U74Av2, C57BL/6 (B6) WT and C57BL/6-Cftr-/- (KO) inbred mice [15].

s – S. E. Choe, Drosophila, Drosophila Gene Collection release 1.0 cDNA clones [19].

t – F. Blattner, E. coli antisense genome, E. coli K-12 strain MG1655 and an isogenic fnr::Sp^rSm^rstrain [47].

u – J. Slonczewski and S. BonDurant, E. coli antisense genome, E. coli K-12 strain W3110 [48].

v1 – E. Blumwald and J. Sottosanto, ATH1, A. thaliana ecotype Wassilewskija, wild-type line (WS), nhx1 'knockout' line, and a knockout restoration line; [49] and unpublished data.

v2 – E. Blumwald and J. Sottosanto, arabidopsis, A. thaliana ecotype Wassilewskija, wild-type line (WS), and a nhx1 'knockout' line (unpublished data).

w – D. Honys and D. Twell, ATH1, Arabidopsis thaliana ecotype Landsberg erecta plants [50].

x – E. Nambara and K. Nakabayashi, ATH1, Arabidopsis thaliana (L.) Heynh of ecotype Columbia [51].

y – E. Nambara and K. Tatematsu, ATH1, Arabidopsis thaliana (L.) Heynh of ecotype Columbia [52].