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FastQC was used for quality analysis of sequencing data.
When extensive unpublished study reports were available, they were used for quality analysis.
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All collected data are later used for quality control analysis.
Next, an unpaired two-group comparison of all six libraries using the mapping results was used for quality control analysis.
Raw data were analyzed initially using Microarray Suite version 5.0 (MAS 5.0, Affymetrix), which was used for quality control analysis, to scale all values to a target value (250), and to generate a list of 'absent' genes.
All code used for quality assessment and data analysis in this study is available at: https://github.com/stephenturner/langouetastrie-scidata2016-chicken-rnaseq-retina-code //github.com/stephenturner/langouetastrie-scidata2016-chicken-rnaseq-retina-code //github.com/stephenturner/langouetastrie-scidata2016-chicken-rnaseq-retina-code //github.com/stephenturner/langouetastrie-scidata2016-chicken-rnaseq-retina-code //github.com/stephenturner/langouetastrie-scidata2016-chicken-rnaseq-retina-code //github.com/stephenturner/langouetastrie-scidata2016-chicken-rnaseq-retina-code
The software tools Feature Extraction 10.7.3.1, GeneSpring GX 11.5.1 and Spotfire Decision Site 9.1.2 (TIBCO) were used for quality control and statistical data analysis.
SRM 1463c was used for quality control of TAs in water analysis.
Standard gases are used for quality control and quality assurance, development of analysis methods and novel air sampling devices.
The control spots present on the slide were used for quality control, but excluded from the further analysis.
The microarray data containing balanced 2-fold differences in the levels of expression of 20% of the genes measured are provided as Supplemental material (Table S1) and may be used by readers for quality analysis estimation of their own analytical methods.
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