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Microarray signals flagged as "not positive and significant" or as "not above significant" were defined as "absent".
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Genes with a fold change (FC) of ≥ 3.0 between the spl5 mutant and the WT were identified as the differential expression genes, but those which have poor microarray signals with the Flag value of A (absent) or with the normalized intensity ≤ 500 were manually eliminated.
The microarray signals were analyzed using the Affymetrix RMA algorithm.
Microarray signals were determined using Affymetrix Microarray Suite 5.1.
To compare qPCR-array and microarray assays, the log2 of microarray signals was used.
Only microarray features flagged as 'good' by GenePix were imported.
After RMA normalization, microarray signal distributions were examined.
We attribute this to a saturation effect in microarray signal.
Microarray signal intensities were normalized using the gcrma package [ 19].
Oligonucleotides with a very low signal for gDNA (corresponding to Signal Noise Ratio - SNR - lower than 2 in more than 75% of microarrays) were flagged and removed from further analysis.
After Lowess slide normalization of the GPR files, any uninformative microarray data were flagged and filtered.
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