ADaCGH results

ADaCGH Results (help)

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Method: DNAcopy

Methods parameters

Minimal common regions

MCR.gapAllowed : 50

MCR.alteredLow : 0.3

MCR.alteredHigh : 0.7

MCR.recurrence : 15

Centering:

Median

Genes/clones per chromosome

Chromosome	Number of genes/clones per chromosome
1	586
2	245
3	217
4	111
5	177
6	192
7	188
8	134
9	299
10	219
11	346
12	198
13	83
14	145
15	116
16	145
17	222
18	58
19	230
20	95
21	41
22	80
23	196

Summary statistics before centering

Array name	Mean	Median	MAD
Subject1	0.012986	0.0155	0.2624
Another	0.025249	0.0180	0.1905
TheThird	0.112556	0.0250	0.3781
Afourth	-0.001935	0.0160	0.2832
Fifth	0.005913	0.0170	0.3025

Summary statistics: subject/array by chromosome before centering

Mean

Chromosome	Subject1	Another	TheThird	Afourth	Fifth
1	0.090423	0.0293642	0.17434	0.07736	4.927e-02
2	-0.074478	0.0133269	-0.01440	-0.06472	-1.012e-01
3	-0.055573	0.0561271	0.07563	-0.03784	-3.970e-02
4	-0.132887	-0.0584339	0.01862	-0.11948	-1.386e-01
5	-0.072078	-0.0007122	0.01901	0.03305	-1.010e-01
6	0.070823	0.0187300	0.05974	0.06398	9.754e-02
7	-0.050175	0.0096525	0.12338	-0.11474	-8.609e-02
8	-0.065189	-0.0175596	-0.03343	0.04949	6.081e-02
9	-0.027570	0.0131310	0.03013	-0.06213	-9.424e-03
10	-0.059386	0.0206537	0.12063	-0.20852	6.389e-02
11	0.025371	0.0265638	0.24991	0.08960	1.905e-01
12	0.052119	0.0249491	0.06638	-0.04875	-3.839e-02
13	0.064910	-0.0508896	0.14996	-0.26021	-1.819e-01
14	-0.012293	0.0491920	0.17089	0.03415	-5.437e-02
15	0.064679	0.0497224	0.13806	0.04573	5.060e-02
16	0.013570	0.1038908	0.14206	0.06914	-1.680e-02
17	0.086739	0.0373194	0.12045	0.05854	-9.384e-06
18	-0.172836	-0.0160517	0.07402	-0.02937	1.138e-01
19	0.218836	0.0349580	0.30589	0.24019	1.979e-01
20	0.096179	0.0485439	0.22176	0.05345	-1.555e-02
21	0.511317	0.0366220	0.40144	0.23049	2.630e-01
22	0.002546	0.0480083	0.22204	0.03595	7.090e-02
23	-0.179891	0.0427844	-0.15123	-0.30251	-3.285e-01

Median

Chromosome	Subject1	Another	TheThird	Afourth	Fifth
1	0.08650	0.01800	0.0720	0.09350	0.068750
2	-0.07300	0.01200	-0.0630	-0.07800	-0.067000
3	-0.04000	0.05400	-0.0560	-0.03750	-0.050000
4	-0.12600	-0.05500	-0.1270	-0.08600	-0.176000
5	-0.06900	0.00200	-0.0940	0.05500	-0.069000
6	0.07850	0.01700	-0.0055	0.07350	0.134000
7	-0.03750	-0.03175	0.0135	-0.12650	-0.098000
8	-0.05362	0.00525	-0.1315	0.02100	0.070000
9	-0.03950	0.00200	-0.0300	-0.08900	0.008000
10	-0.06300	0.00700	-0.0020	-0.16800	0.090000
11	0.04000	0.01500	0.1568	0.11600	0.209000
12	0.02550	0.01367	0.0190	-0.06175	-0.026500
13	0.00100	-0.02600	0.0810	-0.21200	-0.216667
14	-0.02200	0.04200	0.0910	0.04600	-0.044000
15	0.05300	0.07450	0.0260	0.03750	0.043500
16	0.03600	0.08900	0.0900	0.08800	-0.019000
17	0.09700	0.02450	0.0530	0.07950	0.009333
18	-0.19650	-0.04050	-0.0240	-0.05600	0.083500
19	0.20400	0.02500	0.1375	0.23800	0.207000
20	0.08700	0.04500	0.0870	0.07500	-0.003000
21	0.39400	0.03400	0.2860	0.21300	0.251000
22	0.03375	0.03300	0.1310	0.05850	0.044500
23	-0.15675	0.01450	-0.1945	-0.27450	-0.332500

MAD

Chromosome	Subject1	Another	TheThird	Afourth	Fifth
1	0.2491	0.1824	0.3521	0.2335	0.2973
2	0.2283	0.1720	0.4033	0.2713	0.3084
3	0.2446	0.2150	0.3973	0.2602	0.2387
4	0.2898	0.1853	0.3825	0.2105	0.2980
5	0.3099	0.1764	0.3099	0.2446	0.2550
6	0.2120	0.2072	0.3403	0.2320	0.2498
7	0.2291	0.1779	0.3803	0.2580	0.2513
8	0.2365	0.1772	0.3099	0.3069	0.2750
9	0.2409	0.1868	0.3484	0.2884	0.2936
10	0.2891	0.1794	0.3632	0.3010	0.2491
11	0.2128	0.1868	0.4288	0.2335	0.2684
12	0.2387	0.2454	0.3384	0.2535	0.2772
13	0.4863	0.1868	0.5693	0.3099	0.2486
14	0.2624	0.1794	0.4166	0.2669	0.2298
15	0.2724	0.1698	0.3158	0.2417	0.2780
16	0.2209	0.1809	0.3736	0.2333	0.2431
17	0.2457	0.1831	0.3506	0.2520	0.2520
18	0.2528	0.2076	0.3781	0.1972	0.3492
19	0.2787	0.1920	0.4136	0.2128	0.2283
20	0.1913	0.2083	0.2891	0.2002	0.2520
21	0.5085	0.2343	0.3069	0.1853	0.2268
22	0.2065	0.2053	0.3795	0.2083	0.2649
23	0.3132	0.1698	0.5048	0.3662	0.4081

Summary statistics after centering

Array name	Mean	Median	MAD
Subject1	-0.002514	0	0.2624
Another	0.007249	0	0.1905
TheThird	0.087556	0	0.3781
Afourth	-0.017935	0	0.2832
Fifth	-0.011087	0	0.3025

Summary statistics: subject/array by chromosome after centering

Mean

Chromosome	Subject1	Another	TheThird	Afourth	Fifth
1	0.07492	0.011364	0.149342	0.06136	0.03227
2	-0.08998	-0.004673	-0.039402	-0.08072	-0.11818
3	-0.07107	0.038127	0.050625	-0.05384	-0.05670
4	-0.14839	-0.076434	-0.006375	-0.13548	-0.15563
5	-0.08758	-0.018712	-0.005992	0.01705	-0.11797
6	0.05532	0.000730	0.034737	0.04798	0.08054
7	-0.06567	-0.008348	0.098381	-0.13074	-0.10309
8	-0.08069	-0.035560	-0.058426	0.03349	0.04381
9	-0.04307	-0.004869	0.005134	-0.07813	-0.02642
10	-0.07489	0.002654	0.095635	-0.22452	0.04689
11	0.00987	0.008564	0.224906	0.07360	0.17354
12	0.03662	0.006949	0.041378	-0.06475	-0.05539
13	0.04941	-0.068890	0.124965	-0.27621	-0.19887
14	-0.02779	0.031192	0.145890	0.01815	-0.07137
15	0.04918	0.031722	0.113058	0.02973	0.03360
16	-0.00193	0.085891	0.117063	0.05314	-0.03380
17	0.07124	0.019319	0.095454	0.04254	-0.01701
18	-0.18834	-0.034052	0.049020	-0.04537	0.09678
19	0.20334	0.016958	0.280886	0.22419	0.18093
20	0.08068	0.030544	0.196758	0.03745	-0.03255
21	0.49582	0.018622	0.376439	0.21449	0.24601
22	-0.01295	0.030008	0.197040	0.01995	0.05390
23	-0.19539	0.024784	-0.176231	-0.31851	-0.34553

Median

Chromosome	Subject1	Another	TheThird	Afourth	Fifth
1	0.07100	0.000000	0.0470	0.07750	0.051750
2	-0.08850	-0.006000	-0.0880	-0.09400	-0.084000
3	-0.05550	0.036000	-0.0810	-0.05350	-0.067000
4	-0.14150	-0.073000	-0.1520	-0.10200	-0.193000
5	-0.08450	-0.016000	-0.1190	0.03900	-0.086000
6	0.06300	-0.001000	-0.0305	0.05750	0.117000
7	-0.05300	-0.049750	-0.0115	-0.14250	-0.115000
8	-0.06912	-0.012750	-0.1565	0.00500	0.053000
9	-0.05500	-0.016000	-0.0550	-0.10500	-0.009000
10	-0.07850	-0.011000	-0.0270	-0.18400	0.073000
11	0.02450	-0.003000	0.1318	0.10000	0.192000
12	0.01000	-0.004333	-0.0060	-0.07775	-0.043500
13	-0.01450	-0.044000	0.0560	-0.22800	-0.233667
14	-0.03750	0.024000	0.0660	0.03000	-0.061000
15	0.03750	0.056500	0.0010	0.02150	0.026500
16	0.02050	0.071000	0.0650	0.07200	-0.036000
17	0.08150	0.006500	0.0280	0.06350	-0.007667
18	-0.21200	-0.058500	-0.0490	-0.07200	0.066500
19	0.18850	0.007000	0.1125	0.22200	0.190000
20	0.07150	0.027000	0.0620	0.05900	-0.020000
21	0.37850	0.016000	0.2610	0.19700	0.234000
22	0.01825	0.015000	0.1060	0.04250	0.027500
23	-0.17225	-0.003500	-0.2195	-0.29050	-0.349500

MAD

Chromosome	Subject1	Another	TheThird	Afourth	Fifth
1	0.2491	0.1824	0.3521	0.2335	0.2973
2	0.2283	0.1720	0.4033	0.2713	0.3084
3	0.2446	0.2150	0.3973	0.2602	0.2387
4	0.2898	0.1853	0.3825	0.2105	0.2980
5	0.3099	0.1764	0.3099	0.2446	0.2550
6	0.2120	0.2072	0.3403	0.2320	0.2498
7	0.2291	0.1779	0.3803	0.2580	0.2513
8	0.2365	0.1772	0.3099	0.3069	0.2750
9	0.2409	0.1868	0.3484	0.2884	0.2936
10	0.2891	0.1794	0.3632	0.3010	0.2491
11	0.2128	0.1868	0.4288	0.2335	0.2684
12	0.2387	0.2454	0.3384	0.2535	0.2772
13	0.4863	0.1868	0.5693	0.3099	0.2486
14	0.2624	0.1794	0.4166	0.2669	0.2298
15	0.2724	0.1698	0.3158	0.2417	0.2780
16	0.2209	0.1809	0.3736	0.2333	0.2431
17	0.2457	0.1831	0.3506	0.2520	0.2520
18	0.2528	0.2076	0.3781	0.1972	0.3492
19	0.2787	0.1920	0.4136	0.2128	0.2283
20	0.1913	0.2083	0.2891	0.2002	0.2520
21	0.5085	0.2343	0.3069	0.1853	0.2268
22	0.2065	0.2053	0.3795	0.2083	0.2649
23	0.3132	0.1698	0.5048	0.3662	0.4081

Segmented data plots (help)

Smoothed values for all genes/clones are available from file "CBS.output.txt".

Minimal common regions

Case	chromosome	samples	mcr.start	mcr.end
1	1	Fifth,Subject1	19413230	46986933
2	10	Afourth,Subject1	53114789	60260082
3	19	Fifth,Subject1	9816844	11415118
4	19	Fifth,Subject1	11525521	17375378
5	19	Fifth,Subject1	34079100	63761776
6	21	Fifth,Subject1	21835056	35132416
7	21	Fifth,Subject1	36365428	45728946

Download all figures and text results.

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