Profound effect of normalization on detection of differentially expressed genes in oligonucleotide microarray data analysis

Table 1 Results of different methods of statistical analysis

	Invariant feature (AD)	Invariant feature (MBEV)	Invariant set	Global scaling
(a) Mean	3.55	2.45	1.59	3.37
Median	2.09	1.46	1.30	2.12
Max	429.01	667.16	71.63	848.28
(b) Mean FC
F	15.05	9.69	3.06	10.28
KW	18.48	12.24	3.35	12.21
SAM	21.91	13.75	3.63	13.08
Median FC
F	5.77	2.97	2.08	3.89
KW	7.89	3.63	2.25	4.77
SAM	9.20	4.11	2.41	4.92
(c) Mean	428.71	750.20	324.17	384.47
Median	85.52	259.83	122.04	102.37
Max	25141.89	24616.80	28650.70	24794.22
(d) Mean difference
F	2248.04	3346.51	1427.59	1784.93
KW	2545.81	3881.37	1655.16	2044.61
SAM	3157.21	4451.51	1827.97	2216.36
Median difference
F	1116.52	1954.57	664.49	954.38
KW	1328.38	2444.28	815.85	1138.39
SAM	1865.47	2927.57	952.92	1248.04

(a) Mean, median, and maximum fold changes (FC) of all genes on the two array types normalized with different methods. AD, average difference; MBEV, model-based expression values. The averages are given across all genes of the ratio between the maximum and the minimum value across the five different conditions, calculated after averaging replicate arrays. (b) Mean and median fold changes (FC) of genes detected as differentially expressed with 99% confidence by all possible combinations of normalization and statistical analysis algorithms, calculated as in (a). F, F-statistics; KW, Kruskal-Wallis; significance analysis of microarrays (SAM), (c) Mean, median, and maximum signal differences of all genes on the two array types normalized with different methods, calculated by analogy with the ratios in (a). (d) Mean and median signal differences of genes detected as differentially expressed with 99% confidence by all possible combinations of normalization and statistical analysis algorithms, calculated as in (c).

ISSN: 1474-760X