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The extracted intensity data from the mAdb database were normalized by Lowess normalization method and analyzed by modified t-statistic Significance Analysis of Microarrays (SAM) [97].
Illumina GA reads that aligned to the genomic Arabidopsis TAIR9 database were normalized by total reads per million, and analysis was limited to one or more total reads per million in at least one of the five samples.
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Raw data were normalized by quantile normalization.
Microarray data were normalized by quantile normalization.
Gene expression values from the CEL were normalized by use of the standard quantile normalization method in RMA [ 10] and are available from GEO database, accession number GSE9195.
All arrays were normalized by dCHIP and analyzed by GSEA as described (Subramanian et al., 2005), using MSigDB database v3.1 (http://www.broadinstitute.org/gsea/msigdb/index.jsp).jsp
PDFs were normalized by each peak value.
Protein levels were normalized by β-actin.
Peptides were normalized by OD 280nm.
Emission values were normalized by protein concentration.
Data were normalized by Renilla luciferase.
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