Preferred analysis methods for Affymetrix GeneChips revealed by a wholly defined control dataset

Table 1 The number of clones and assigned fold change for each pool of PCR products

Pool number	Number of clones	Number of assigned Affymetrix probe sets	Assigned fold change (S vs C)	Amount of RNA added to each C chip (μg)	Amount of RNA added to S chip (μg)
1	87	84	1.2	0.47	0.56
2	141	143	2	0.43	0.85
3	85	83	1.5	0.35	0.52
4	180	185	2.5	0.73	1.82
5	90	89	1.2	0.29	0.35
6	88	96	3	0.65	1.94
7	186	188	3.5	0.76	2.67
8	90	95	1.5	0.44	0.67
9	180	190	4	0.78	3.11
10	183	191	1.7	0.48	0.81
13	391	385	1	0.37	0.37
14	369	355	1	1.23	1.23
15	394	404	1	0.40	0.40
16	452	453	1	0.57	0.57
17	419	434	1	0.44	0.44
18	372	407	1	0.31	0.31
19	163	191	1	0.27	0.27

Also depicted is the total amount of cRNA for each pool that was placed on each chip, and the number of Affymetrix probe sets that are assigned to each pool. There were 10,131 probe sets not assigned to any spiked-in clone (called empty). Pools 11 and 12 were not included in this dataset.

ISSN: 1474-760X