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Currently, microarrays are unable to efficiently deal with "drop-outs," when one or more spots on the array are corrupted.
A computer records positive hits by checking for bright spots on the array.
But tests on the second strain--YJM789--revealed over 3000 spots on the array with little fluorescence, denoting mismatches, or differences, with the reference strain.
Duplicated spots on the array allowed for evaluation of signals and exclusion of errors.
This potentially saves 85,152 spots on the array for additional probes and affords the possibility of cutting costs by moving to a smaller platform altogether.
This calculation was based on the signals from a set of negative control spots on the array containing oligos from humans or plants that should not hybridize to bacterial RNA.
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Control and empty spots on the arrays were not included for analysis, and spots flagged as bad spots on visual inspection of the arrays were also excluded.
Three of these genes occupied neighbouring spots on the arrays.
Approximately 70% of all spots on the arrays were retained after filtration and normalization.
Spots on the arrays were quantified by BD AtlasImage™ 2.7 software (Clontech, Palo Alto, CA).
The values of all the spots on the arrays were per spot and per chip intensity dependent (Lowess) normalized.
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