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Only microarray features flagged as 'good' by GenePix were imported.
Microarray features flagged by the Genepix software, designated as empty (no oligo probe), not in genome, negative control, positive control, plastid genome, unmapped, or mapping to non-mRNA were given zero weight for normalization using the modifyWeights function in limma.
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Features flagged in Feature Extraction as Feature Noutliersrm outliers were excluded.
Features flagged in Feature Extraction as Feature Noutliersrm outliers were excluded [ 37].
Microarray features that received a "−100" flag by the scanning software GenePix or that had a median fluorescence intensity <300 were removed from the analysis [44].
The microarray features were filtered according to the Agilent quality control flags: if the feature was determined to be well above background, if the noise did not exceed a threshold, and if it was not saturated (IsNOTWellAboveBG, IsSaturated and IsFeatNonUnifOL [ 65]) in at least 10%% of the total microarray count, then that particular microarray feature was retained for further analysis.
A complete description of the microarray features can be found.
Microarray features were extracted using Agilent Feature Extraction software version 10.5.1.1.
Microarray signals flagged as "not positive and significant" or as "not above significant" were defined as "absent".
After Lowess slide normalization of the GPR files, any uninformative microarray data were flagged and filtered.
Only one microarray assay was flagged for poor performance in this study: Sample A, Method 1 (no depletion_Affymetrix).
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