Assessing affymetrix GeneChip microarray quality

BMC Bioinformatics

Table 1 Q-values for True Positives

	Original	1	2	3	4	5	6	7	8
546_at	<0.01	<0.01	<0.01	<0.01	<0.01	<0.01	<0.01	<0.01	0.01
36311_at	<0.01	0.02	0.02	0.03	<0.01	<0.01	0.02	0.04	0.01
36889_at	<0.01	<0.01	0.03	0.03	<0.01	0.02	0.06	0.04	0.02
1091_at	<0.01	0.02	0.02	0.03	<0.01	0.01	0.02	0.02	0.01
39058_at	<0.01	0.02	0.02	0.03	<0.01	0.01	0.02	0.04	0.02
1024_at	<0.01	0.05	0.05	0.04	<0.01	0.02	0.1	0.1	0.02
37777_at	0.02	0.07	0.17	0.09	<0.01	0.1	0.31	0.42	0.04
684_at	0.02	0.08	0.13	0.09	<0.01	0.1	0.11	0.13	0.06
33818_at	0.08	0.11	0.24	0.49	<0.01	0.85	0.84	0.85	0.75
407_at	0.39	0.58	0.64	0.67	0.14	0.85	0.84	0.64	0.76
36202)_at	0.52	0.58	0.64	0.67	<0.01	0.85	0.84	0.85	0.76
1597_at	0.75	0.58	0.64	0.67	0.73	0.85	0.84	0.85	0.76
38734_at	0.75	0.58	0.64	0.67	0.46	0.85	0.84	0.85	0.76
36085_at	0.75	0.58	0.64	0.67	0.46	0.85	0.84	0.85	0.76
40322_at	0.75	0.58	0.64	0.67	0.46	0.85	0.84	0.85	0.76
1708_at	0.75	0.58	0.64	0.67	0.61	0.85	0.84	0.85	0.76

The q-values for each of the 16 spiked in probesets using all 8 arrays (Column 1) and with each of the 8 arrays removed (Columns 2-9). A q-value < 0.01 denotes a probeset correctly identified as differentially expressed. Removing the poor quality array (4) decreases the q-values, while removing the other good quality arrays increases the q-values.

ISSN: 1471-2105