Effect of various normalization methods on Applied Biosystems expression array system data

BMC Bioinformatics

Table 4 Differential expression t-test, t-test + FDR, t-test + FC, t-test + FDR + FC cut, SAM applied to Quantile normalized data.

Method	TP	TP rate	TN	FP	FDR	FN
TaqMan	763	0	85	0	0	0
p-t test	558	73.13	55	30	5.10	205
p-t test + FDR	549	71.95	56	29	5.02	214
p-t test + FC	483	63.30	64	21	4.17	280
p-t test +FDR+FC	479	62.78	64	21	4.20	284
SAMq	508	66.58	63	22	4.15	255

We use different methods to detect significantly differentially expressed genes for data Quantile normalized: (1) t-test (p-value < 0.05), (2) t-test controlling FDR at 5% level, (3) t-test (p-value < 0.05) and FC < 1.5, (4) t-test controlling FDR at 5% level and FC < 1.5, or (5) SAM q < 0.05. We compare the results for data generated by site 1, from each normalization method, with the ones from TaqMan^® assays for which differential expression is detected using t-test and controlling FDR at 5% level. We keep track of up/down regulation in each platform.

ISSN: 1471-2105