Data was read into R and normalized within arrays using median normalization and between arrays using Aquantile normalization from the Limma package [56].
Between-array median normalization was carried out and significantly deregulated miRNAs were computed using the Significant Analysis of Microarray (SAM; http://www-stat.stanford.edu/~tibs/SAM/) method.
Microarray data were normalized using median normalization method.
For the Affymetrix dataset, results were compared between the dataset normalized with MAS 5.0 alone and MAS 5.0 + NEPS scaling and for the Agilent dataset, the comparison was done between median normalization alone and NEPS scaling followed by median normalization.
Expressed data were normalized using median normalization.
The expression data were normalized using median normalization.
Data were normalized using median normalization across the array.
To allow comparison of ratios between the two experiments, spot volume data for the two fluorescence channels were first normalized by median normalization (Keeping and Collins, 2011) using the median values for the first experiment as a reference.
Median normalization of the RPKM values between timecourse biological replicates was performed in R. Resulting RPKMs were log2 transformed with respect to the 0 hr ethylene treatment wild-type Col-0 EIN3 ChIP.
Expressed data were normalized using the Median normalization.
