Biotools

BioTools

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:

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

Sequence manipulation and data Restriction digest Pcr amplification
Chaos game representation Melting temperature Protein properties
Reduce protein alphabet Seq alignment Dna to protein Skews
Microarray analysis adaptive quantification Distance among sequences
Oligonucleotide frequency Protein to dna Random seqs
Microsatellite repeats finder Find palindromes