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More sample pre-processing information can be found in Additional file 1.
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The preliminary results showed the need for further investigations based on a robust experimental design and sample pre-processing.
Sample pre-processing and biotin labeling were performed using the Affymetrix GeneChip® cDNA Synthesis Kit and IVT Labeling Kit (Affymetrix) according to the manufacturer's protocols.
Sample pre-processing and hybridisation was performed as per manufacturer's recommendations.
Following initial within-sample pre-processing, three cross-platform normalisation techniques, (Standardisation, ComBat [7] and XPN [8]), were applied, resulting in 9 normalised datasets.
More elaborate pre-processing methods may help remove the influence of the background, scattering and noise.
More details on pre-processing and annotation are given in the Supplementary Methods.
Now, we have one more pre-processing step to save data at the border of CGH data.
Then adaptive temporal sampling will be applied, which is introduced in Section "Adaptive temporal sampling in pre-processing".
The sequence coverage is more sensitive to the pre-processing parameters.
More samples increase the processing time.
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