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All probes were screened for quality and replicated on the array.
However, due to unused space, there were 255 probes that were replicated on the array (7 of these are in triplicate).
Feature-to-feature reproducibility was verified via a correlation analysis of filtered log2 ratios for 384 probes that are replicated on the array.
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Additional file 5: Raw microarray data of all spot replicates on the array.
Technical replicates on the same array were combined.
All probes are replicated once on the array for a total of over 385,000 probes synthesized in situ on glass slides [ 64].
Within the design each oligonucleotide was replicated on each array to provide greater statistical measurement for each gene.
100 μl was loaded into each of the 8 ports of the array (2 ports comprise of one sample replicate on the array).
To eliminate the replication imbalance and to put all genes on the same replication level, genes with replicates on the array were averaged and the average was considered as one feature for the analysis.
Finally, quality control statistics were computed using a variety of Illumina's internal control probes that are replicated on each array.
Variation among feature replicates on the array was calculated by conversion of raw data to log-ratios.
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