Microarray amplification bias: loss of 30% differentially expressed genes due to long probe – poly(A)-tail distances

Table 2 Randomized hybridization design on Agilent WHG arrays

Data set	Sample	Number of amplification rounds	Dye label	Array number
1	T1	1x	Cy3	3
2	T1	1x	Cy5	1
3	T2	1x	Cy3	1
4	T2	1x	Cy5	2
5	B	1x	Cy3	2
6	B	1x	Cy5	3
7	T1	2x	Cy3	6
8	T1	2x	Cy5	4
9	T2	2x	Cy3	4
10	T2	2x	Cy5	5
11	B	2x	Cy3	5
12	B	2x	Cy5	6

T1, microdissected tumor sample; T2, duplicate microdissected tumor sample; B, microdissected bronchial epithelial sample.

ISSN: 1471-2164

Data set	Sample	Number of amplification rounds	Dye label	Array number
1	T1	1x	Cy3	3
2	T1	1x	Cy5	1
3	T2	1x	Cy3	1
4	T2	1x	Cy5	2
5	B	1x	Cy3	2
6	B	1x	Cy5	3
7	T1	2x	Cy3	6
8	T1	2x	Cy5	4
9	T2	2x	Cy3	4
10	T2	2x	Cy5	5
11	B	2x	Cy3	5
12	B	2x	Cy5	6

Data set	Sample	Number of amplification rounds	Dye label	Array number
1	T1	1x	Cy3	3
2	T1	1x	Cy5	1
3	T2	1x	Cy3	1
4	T2	1x	Cy5	2
5	B	1x	Cy3	2
6	B	1x	Cy5	3
7	T1	2x	Cy3	6
8	T1	2x	Cy5	4
9	T2	2x	Cy3	4
10	T2	2x	Cy5	5
11	B	2x	Cy3	5
12	B	2x	Cy5	6

Data set	Sample	Number of amplification rounds	Dye label	Array number
1	T1	1x	Cy3	3
2	T1	1x	Cy5	1
3	T2	1x	Cy3	1
4	T2	1x	Cy5	2
5	B	1x	Cy3	2
6	B	1x	Cy5	3
7	T1	2x	Cy3	6
8	T1	2x	Cy5	4
9	T2	2x	Cy3	4
10	T2	2x	Cy5	5
11	B	2x	Cy3	5
12	B	2x	Cy5	6