As the reflectance spectra are previously normalized using a reflectance standard, further intensity scaling is not required.
Each CT was previously normalized using the expression levels of ACT2 (At3g18780), PPR (At5g55840), and UPL7 (as3g53090) as internal references.
The data were previously normalized using robust multi-array average (RMA) method, according to ftp://ftp.arabidopsis.org/home/tair/Microarrays/analyzed_data/README.org/home/tair/Microarrays/analyzed_data/README
Residuals were thus derived for each trait and were normalized using an inverse normal transformation, as previously advocated [ 22, 23].
Data were normalized using the normalization factors previously used for the whole transcriptome analysis (Manfrini et al., 2015), based on the total number of reads that mapped on all the ORFs of the yeast genome.
The Affymetrix gene expression profiling data was normalized using the previously published Robust Multi-array Average (RMA) algorithm using the GeneSpring 7 software (Agilent, Palo Alto, CA).
Pre- and post-scan MD images were segmented and normalized using a previously described diffeomorphic anatomical registration through exponentiated lie algebra (DARTEL -based methoDARTEL -basedt al. 2013b), which provided imethodof 1.5 × 1.5 × 1.5 mm voxels.
Hybridization signals were normalized using the scale normalization procedure previously described [ 25].
The Illumina data were then normalized using the 'normalize quantiles' function in the BeadStudio Software.
