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The morphology of the microarray spots was similar to those previously described [19] (Figure 3).
We did so in order to determine whether the absence of hybridization signals for some microarray spots was due to the absence of any DNA there, which would indicate a defect in the manufacturing of the microarray at those spots.
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The segmentation of cDNA microarray spots is essential in analyzing the intensities of microarray images for biological and medical investigation.
Microarray spots were combined and signals were normalized using polynomial normalization against the median of each probe in the 7 samples.
Microarray spots were combined and signals normalized as described previously (21).
At least two representative tissue microarray spots were counted from each tumour.
Signals intensities from microarray spots were quantified using GenePix Pro software (Axon Instruments) and data analyzed using Microsoft Excel®.
Dye-normalised fluorescent intensities of individual microarray spots were extracted using the Agilent Feature Extraction software 9.5.
Interpreting presence or divergence of genes using a multistrain microarray in the absence of a reference for all microarray spots is highly complex as illustrated in this study.
The microarray spots were located by using the GenePix Pro 6.0 software package (Axon Instruments, Foster City, CA) together with the array list file [ 67].
Re-sequenced array plates are compared using pair-wise BLAST [ 42] against previous sequencing results so that the identity of printed microarray spots are verified.
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