A normalization strategy applied to HiCEP (an AFLP-based expression profiling) analysis: Toward the strict alignment of valid fragments across electrophoretic patterns

Table 1 Calculation of quality scores for lane 0 h-1 in Fig. 1. Similarity scores (S) are computed using Equation 3. The quality score at fragment length L₄ is calculated as (0.00 + 0.17 + 0.04 - 0.27)/4 = -0.02. The quality profile for each lane is made by spline interpolation of a set of quality scores of fragment lengths of peaks in the lane.

i	L _i	σ _i	S¹ in size interval [L_i-j- 2.5 σ _i-j, L_i-j+4+ 2.5 σ_i-j+4]					Q(L_i)
			j = 0	j = 1	j = 2	j = 3	j = 4
1	38.28	0.145	-0.27	-	-	-	-	-0.27
2	39.16	0.143	0.04	-0.27	-	-	-	-0.11
3	40.17	0.186	0.17	0.04	-0.27	-	-	-0.02
4	41.06	0.212	0.00	0.17	0.04	-0.27	-	-0.02
5	42.07	0.223	0.02	0.00	0.17	0.04	-0.27	-0.01
6	44.05	0.221	-0.36	0.02	0.00	0.17	0.04	-0.03
7	45.13	0.190	-0.28	-0.36	0.02	0.00	0.17	-0.09
8	46.05	0.149	0.52	-0.28	-0.36	0.02	0.00	-0.02
9	46.80	0.215	0.59	0.52	-0.28	-0.36	0.02	0.10
10	48.48	0.240	0.74	0.59	0.52	-0.28	-0.36	0.24
11	49.41	0.242	0.69	0.74	0.59	0.52	-0.28	0.45
12	54.95	0.320	0.49	0.69	0.74	0.59	0.52	0.61
13	56.09	0.215	0.30	0.49	0.69	0.74	0.59	0.56
14	57.54	0.152	0.39	0.30	0.49	0.69	0.74	0.52
15	59.00	0.195	0.41	0.39	0.30	0.49	0.69	0.45
16	60.05	0.252	0.39	0.41	0.39	0.30	0.49	0.40
17	62.41	0.222	0.32	0.39	0.41	0.39	0.30	0.36
18	67.55	0.135	0.43	0.32	0.39	0.41	0.39	0.39
19	68.26	0.259	0.47	0.43	0.32	0.39	0.41	0.40
20	69.76	0.216	0.57	0.47	0.43	0.32	0.39	0.43

ISSN: 1471-2105