Microarray Data Analysis: adaptive quantification method

Microarray Data Analysis

Spots are analyzed by the adaptive quantification method with local background subtractions

Microarray data:

Column	Row	Name	F532 Median	B532 Median	F635 Median	B635 Median
1	1	Control -	1145	160	1182	122
2	1	Control -	593	218	515	122
3	1	Control -	1257	183	1382	128
4	1	Control -	525	168	475	126
5	1	Control -	1132	155	1271	120
6	1	Control -	610	218	510	122
7	1	Control -	1099	176	1292	127
8	1	Control -	603	180	481	123
9	1	Control -	878	149	1082	119
10	1	Control -	441	139	444	119
1	2	Control +	10387	140	4269	116
2	2	Control +	9035	132	3705	115
3	2	Control +	7899	126	3331	117
4	2	Control +	7039	118	2883	114
5	2	Control +	9407	138	3994	115
6	2	Control +	7545	127	3240	116
7	2	Control +	8915	134	3843	114
8	2	Control +	7169	126	3038	119
9	2	Control +	7867	137	3345	120
10	2	Control +	9369	140	4184	122
1	3	Gene 1	4276	111	574	108
2	3	Gene 1	3798	111	439	107
3	3	Gene 1	3311	110	418	107
4	3	Gene 1	4258	109	441	106
5	3	Gene 1	3548	109	445	104
6	3	Gene 1	3448	108	424	101
7	3	Gene 1	3412	107	415	105
8	3	Gene 1	3856	106	445	107
9	3	Gene 1	3510	116	395	111
10	3	Gene 1	3853	108	427	109
1	4	Gene 2	4830	119	670	107
2	4	Gene 2	5625	101	804	103
3	4	Gene 2	5053	118	682	105
4	4	Gene 2	5895	106	835	105
5	4	Gene 2	5913	102	816	105
6	4	Gene 2	5041	103	773	103
7	4	Gene 2	4846	114	703	106
8	4	Gene 2	5362	107	812	108
9	4	Gene 2	4811	117	716	104
10	4	Gene 2	4610	109	627	108
1	5	Gene 3	431	99	427	107
2	5	Gene 3	536	90	520	105
3	5	Gene 3	528	100	475	109
4	5	Gene 3	489	92	504	105
5	5	Gene 3	509	93	508	108
6	5	Gene 3	486	92	523	107
7	5	Gene 3	605	104	574	111
8	5	Gene 3	562	97	638	109
9	5	Gene 3	591	108	577	112
10	5	Gene 3	609	101	626	110
1	6	Gene 4	30728	202	3353	130
2	6	Gene 4	41199	206	4245	131
3	6	Gene 4	22218	206	2434	128
4	6	Gene 4	30179	199	3062	122
5	6	Gene 4	26642	170	2525	122
6	6	Gene 4	23061	184	2259	119
7	6	Gene 4	29017	183	2782	114
8	6	Gene 4	27071	176	2747	116
9	6	Gene 4	22631	164	2345	110
10	6	Gene 4	23668	191	2559	113
1	7	Gene 5	3190	103	2135	104
2	7	Gene 5	3294	106	2389	100
3	7	Gene 5	2114	106	1769	107
4	7	Gene 5	3029	103	2524	105
5	7	Gene 5	3236	105	2237	103
6	7	Gene 5	3296	106	2379	104
7	7	Gene 5	3131	117	2416	110
8	7	Gene 5	3261	112	2440	108
9	7	Gene 5	2866	111	2469	107
10	7	Gene 5	2621	116	2057	111
1	8	Gene 6	3791	111	3077	109
2	8	Gene 6	4054	112	3210	107
3	8	Gene 6	3235	115	2362	112
4	8	Gene 6	3874	117	3070	105
5	8	Gene 6	4208	101	3399	109
6	8	Gene 6	3283	117	2779	108
7	8	Gene 6	3354	109	2403	105
8	8	Gene 6	4139	104	3307	108
9	8	Gene 6	2706	108	2046	108
10	8	Gene 6	3027	101	2693	105
1	9	Gene 7	979	98	805	108
2	9	Gene 7	877	95	766	106
3	9	Gene 7	877	98	798	110
4	9	Gene 7	932	94	791	105
5	9	Gene 7	941	95	873	111
6	9	Gene 7	995	96	943	110
7	9	Gene 7	967	109	861	112
8	9	Gene 7	1073	101	926	109
9	9	Gene 7	984	109	893	111
10	9	Gene 7	976	106	901	110
1	10	Gene 8	215	194	152	124
2	10	Gene 8	212	187	126	120
3	10	Gene 8	276	201	177	131
4	10	Gene 8	205	188	139	124
5	10	Gene 8	227	186	137	121
6	10	Gene 8	223	209	137	123
7	10	Gene 8	214	182	139	116
8	10	Gene 8	189	168	129	114
9	10	Gene 8	217	167	163	115
10	10	Gene 8	247	179	156	118

Copy tabulated data to the textarea as shown. First valid data must correspond to Column 1/Row 1.
All lines preceding data for Column 1/Row 1 will be removed previous to calculations.

Computational procedure:
  1. For each spot, the following is computed for both channels (1 and 2): (value-background)*100/sum(value-background))
  2. With previous results, ch1/ch2 and ch2/ch1 are computed
  3. As there are several replicas for ch1/ch2 and ch2/ch1, median and its base 10 logarithm is computed.
  4. In a table, medians and logs are represented. A color code is used to show over-expression (red) or under-expression (blue).

Source code available at biophp.org