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GenePix™ Analysis Software was used for spot detection and quantification and also for spot quality flagging.
Normalization was done with GenePix software using the mean of the median of ratios of all the autosomal features in the array, excluding those removed by the quality flagging scripts.
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After logarithm transformation of ratio of median of the intensities (without background substraction) in the two channels, data were weighted to penalize spots of poor quality, flagged, or spots for which intensities in the two channels were close to background (median of intensity less than median of background plus 2 standard deviations for both Cy3 and Cy5 signals).
First, reads longer than 50 nt flagged with Illumina's low quality flag "B" were removed from all datasets.
Each instrument has a quality flag in the event packet.
Only events with quality flag A B were accepted.
The S-WPIA ignores the event packet when the quality flag shows bad-quality data.
High accuracy of the FGM magnetometer readings (quality flag 1 set to 0) and dual star-camera mode (quality flag 2 set to 3).
Quality A quality flag whose values indicate any issues with the model (zero indicates 'no issues').
the quality flags should indicate data of a minimum quality threshold.
Data associated with a TII quality flag ≥20 are indicated in blue.
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CEO of Professional Science Editing for Scientists @ prosciediting.com