A generally applicable validation scheme for the assessment of factors involved in reproducibility and quality of DNA-microarray data

Table 2 Contribution of sources to the variance estimated for the nine validation experiments (Figure 4) and contribution of individual factors to the VG interaction^a.

Variance source	Contribution to the variance (%)
Gene (G)	5.0
Dye (SG)	4.2
Gene × Array^b	7.8
RNA isolation and labeling^c	1.5
Sampling	7.1
VG ^d	26.9
Day × Gene	19.7^e
Experimenter × Gene	17.3^e
Array batch × Gene	14.9^e
Spot pins × Gene	4.5^f

^a The degrees of freedom results in the separate ANOVAs are listed in the supplementary web-site [21].
^b Assumed to consist of hybridization effects and signal-to-noise differences per slide.
^c Derived from the variance observed between B^a and B^b cultures (Figure 1).
^d Variances that are dependent on the validation experiment performed and due to day-to-day differences, identity of the experimenter, and DNA microarray batch differences.
^e Due to overlap in levels, the contribution of these interactions were individually determined.
^f A change from 8 to 12 spot-pins used for array spotting coincided with a switch in the RNA isolation method.

ISSN: 1471-2164