Characterization and simulation of cDNA microarray spots using a novel mathematical model

BMC Bioinformatics

Table 1 Estimated values of the four parameters of the three types of spot shapes of Image I *

Spot shape		x ₀	K	a	K _V	MSD***
doughnut	1	101.06	5.67E-3	-0.40	1.74	3.01E-2
	2	540.79	6.35E-3	-0.77	0.41	4.58E-3
	3	635.04	7.35E-3	-0.47	0.71	2.71E-2
	4	686.56	5.66E-3	-0.51	0.44	5.24E-3
	5	777.05	2.73E-3	-0.56	0.64	1.69E-2
	mean	548.10	5.55E-3	-0.54	0.79	1.68E-2
	SD**	264.12	1.72E-3	0.14	0.55	1.19E-2
volcano	1 ^†	599.58	2.76E-3	-0.55	2.45	8.12E-4
	2 ^†	265.87	1.61E-3	0.70	2.82	8.96E-3
	3 ^†	401.92	1.59E-3	-0.72	0.60	3.50E-3
	4 ^††	32.69	5.23E-3	0.14	3.31	4.21E-3
	5 ^††	27.10	7.30E-3	0.65	5.43	4.57E-4
	mean	265.43	3.70E-3	0.04	2.92	3.59E-3
	SD**	245.59	2.50E-3	0.66	1.74	3.42E-3
peak	1	39.41	2.55E-4	0.04	4.59	2.26E-2
	2	39.87	2.90E-4	0.18	1.12	1.14E-3
	3	37.51	8.42E-4	0.22	2.68	7.56E-3
	4	37.59	8.41E-4	0.22	2.21	1.13E-3
	5	41.39	2.24E-4	0.86	2.45	1.06E-2
	mean	39.15	4.90E-4	0.30	2.61	8.61E-3
	SD**	1.64	3.21E-4	0.32	1.26	8.83E-3

* This image was obtained from Stanford MicroArray Database [38]: Experiment ID, 50150; Experiment name, MMAF array batch on PLL QC-1; Category, Quality Control; Subcategory, Array Batch QC; Slide name, mmaf042.
** Standard deviation.
*** Mean squared deviation, $MSD = \frac{1}{N} \sum_{i = 1}^{N} {(y_{i} - x_{i})}^{2}$ .
^† The spot shape was close to the doughnut-shape.
^†† The spot shape was close to the peak-shape.

ISSN: 1471-2105