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Microarray fluorescence signals were normalized using Robust Multiarray Average [34].
The microarray fluorescence signals were normalized using the GeneChip Operation Software GCOSS ver. 1.4, Affymetrix).
Microarray fluorescence signals were normalized using a global loess algorithm in R2.14.1 with the Linear Models for Microarray Data (limma) package [ 62].
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These GMOs could also be quantified using the microarray, as their fluorescence signals increased linearly with GMO concentration.
Finally, the microarrays were washed and fluorescence signals of the hybridized Agilent Microarrays were detected using Agilent's Microarray Scanner System.
After hybridization and washing according to published procedures [43], the microarrays were scanned for fluorescence signals using a Genepix 4000B laser scanner.
Therefore, amplification of mRNA sample is necessary before performing microarray experiment to detect the fluorescence signals of mRNA [ 1- 4].
The same figure also appears with other public chicken microarray datasets: the fluorescence signal on our arrays hybridized with penguin RNA is relatively low compared with arrays hybridized with chicken RNA, as expected.
Briefly, the fluorescence signals of the microarray were scanned and saved as DAT image files.
Fluorescence signals of the hybridized Agilent Microarrays were detected using Agilent's Microarray Scanner System.
Fluorescence signals of the hybridized Agilent Microarrays were detected using Agilent's Microarray Scanner System (Agilent Technologies).
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