Variation in fiberoptic bead-based oligonucleotide microarrays: dispersion characteristics among hybridization and biological replicate samples

doi:10.1186/1745-6150-1-18

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Variation in fiberoptic bead-based oligonucleotide microarrays: dispersion characteristics among hybridization and biological replicate samples

Jaroslav P Novak¹ , Merrill C Miller III² and Douglas A Bell²

¹McGill University and Genome Quebec Innovation Centre, 740 Dr. Penfield, Montreal, Quebec, H3A 1A4, Canada

²Environmental Genomics Section, Laboratory of Molecular Genetics, C3-03, PO Box 12233, National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709, USA

author email corresponding author email

Biology Direct 2006, 1:18doi:10.1186/1745-6150-1-18


Published:	20 June 2006

Additional files

Additional file 1:

Supplemental Figure S1, comparison of the pooled reference samples C5a and C5b before renormalization. Dispersion pattern and 0.9 probability interval, before normalization.

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Additional file 2:

Supplemental Figure S2, comparison of the pooled reference samples C5a and C5b before renormalization. Running mean of 90 genes, before renormalization.

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Additional file 3:

Supplemental Figure S3, comparison of the pooled reference samples C5a and C5b after renormalization. Dispersion pattern and 0.9 probability interval, after normalization.

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Additional file 4:

Supplemental Figure S4, comparison of the pooled reference samples C5a and C5b after renormalization. Running mean of 90 genes, after renormalization.

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Additional file 5:

Supplemental Figure S5, quantile-quantile plot of the frequency distribution. Comparison of the observed expressions with the corresponding inverse normal distribution, combined samples C1a, C2a, C3a, C4a, C5a: range of average expressions from 0.1 to 2.0; figure shows the relative values (expressions divided by the mean of five arrays).

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Additional file 6:

Supplemental Figure S6, quantile-quantile plot of the frequency distribution. Comparison of the observed expressions with the corresponding inverse normal distribution, combined samples C1a, C2a, C3a, C4a, C5a: range of average expressions from 117 to 5432.

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Additional file 7:

Supplemental Table S1, same-type sample dispersion parameters for the glucose oxidase treatment assay. Coefficients of the standard deviation function a and b and K_αcoefficient corresponding to 0.9 probability interval; nt and tr stand for "untreated" and "treated," respectively.

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Additional file 8:

Supplemental Table S2, dispersion parameters for case/control comparisons in the glucose oxidase treatment assay. Coefficients of the standard deviation function a and b and K_αcoefficient corresponding to 0.9 probability interval; nt and tr stand for "un-treated" and "treated," respectively.

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Additional file 9:

Supplemental Table S3, differentially expressed genes selected by the Illumina custom algorithm. Probe sets selected by the Illumina method. The table shows the gene name and function, mean intensity, coefficient of variation and Illumina differential score; value ± 20 corresponds to P = 0.01. Note that Illumina uses different normalization and, consequently, the mean intensities of Tables 3 and 4 do not agree. Bold print indicates the probe sets selected by the consecutive sampling method and coincidence test.

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