Data analysis was performed using Feature Extraction and Image Analysis software (Agilent Technologies Inc). and Microarray Suite (Affymetrix, Santa Clara, CA), and normalized and processed as described (Hanada et al. [2013]).
The gene expression levels of samples were normalized and analyzed by using Microarray Suite, MicroDB™, and Data Mining Tool software (Affymetrix, Santa Clara, CA).
Genes that responded to the various light and/or carbon treatments (C, LC, or L) were further identified and classified based on parameters assigned to each gene by Microarray Suite 5.0 and using a 'metric' classification system as described in Methods.
The array expression values were generated using Affymetrix Microarray Suite 5.0 and dChip analyzer 1.3.
The GeneChips data analysis was performed using the Affymetrix Microarray suite 5 and the GeneSpring 5 (Agilent Technologies, Palo Alto, CA) analysis package.
Gene expression was then quantified by using Microarray Suite, MicroDB™, and Data Mining Tool Software (Affymetrix, Santa Clara, CA).
Data analysis was performed in the Microarray Suite 5 and Data Mining Tool, v3 (Affymetrix).
The resultant output was analyzed using Affymetrix Microarray Suite software and examined for excessive background or evidence of RNA degradation.
Microarray analysis was performed using Affymetrix MicroArray Suite 5.0 and an in-house Visual Basic software MATRIX 1.24 (Girard et al, manuscript in preparation).
Transcripts that were absent across all experiments were identified using Absent/Present calls (Microarray Suite 5.0) and filtered for transcripts that were not expressed in any experiment.
