Error, reproducibility and sensitivity: a pipeline for data processing of Agilent oligonucleotide expression arrays

Table 1 Intra and inter array variation, before and after normalisation

	Within Array¹	Log transformed without normalisation²	Log transformed with linear regression normalisation^2,3	Log transformed with LOESS linear regression normalisation^2,3
SD Cy5	0.20	0.91	0.56	0.52
SD Cy3	0.16	0.56	0.31	0.24
Correl Cy5:Cy3	0.84	0.53	0.45	0.40
CoVar Cy5:Cy3	0.02	0.34	0.11	0.09
SD Cy5/Cy3⁴	0.13	0.64	0.43	0.38

1. The SD for Cy3 and Cy5, and the correlation and covariance between Cy3 and Cy5 signals, was calculated across all replicates for each probe which is represented by multiple within array replicates. The Table shows the average of these SDs for all this subset of replicated probes, from a random sample of five arrays.
2. The SD for Cy3 and Cy5, and the correlation and covariance between Cy3 and Cy5 signals, was calculated for each probe across all 77 arrays, and then averaged across all probes.
3. The data were first normalised as detailed in Text and Legend to fig 2
4. The SD of the ratio of Cy5/Cy3 signal was calculated using equation 1 in text.

ISSN: 1471-2105