Normalization of low-density microarray using external spike-in controls: analysis of macrophage cell lines expression profile

Table 3 ANOVA analysis before and after normalization

	Before normalization				After normalization
Source of variation^a)	sum of squares	degree of freedom	p-value	% of variance	sum of squares	degree of freedom	p-value	% of variance
Spike concentration^b)	169.084	3	0.000	48.3%	0.762	3	0.000	1.0%
Spike characteristics^c)	62.295	7	0.000	17.8%	50.094	7	0.000	40.4%
Array position^d)	1.530	11	0.000	0.4%	1.247	11	0.000	0.6%
Concentration* characteristics^e)	104.040	21	0.000	29.7%	58.848	21	0.000	47.4%
Error^f)	13.477	1240		3.8%	13.105	1240		10.6%
Total^g)	332.992	1282			119.280	1282
	R Squared^h) = 0.958				R Squared^h) = 0.887

^a) The variability is subdivided into independent variances. ^b) Amount of spikes in the experiment. ^c) Base composition, length of the mRNA and interaction with other RNA molecules. ^d) Spot size, tips, slide homogeneity, printer accuracy. ^e) Interaction between spike concentration and spike characteristics. ^f) Residual variability. ^g) Corrected total variability. ^h) R squared calculated from linearity test resulting from the amount of variance in the dependent variable that is accounted for by the corrected model.

ISSN: 1471-2164