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The data images produced by the microarray scanning were interpreted by Affymetrix® Microarray Suite 5.0 (MAS 5.0) software with scaling of all probe sets to a target value of 500.
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The microarray scanning profiles were processed by Agilent Feature Extraction 10.7.3.1.
Intensity extraction from the microarray scan images was accomplished by the fixed circle quantification method using QuantArray (PerkinElmer Life Sciences).
The microarray scan data were analyzed by Agilent's Feature Extraction software, which estimates the background level and gives a feature-specific background cut-off level per chip.
However, detection of this mRNA on the microarray scan and its subsequent verification by RT-PCR analysis indicates the sensitivity of the microarray assay.
Furthermore, examination of contamination by leukocytes (Fig. 5b, c) and the presence of malaria-infected erythrocytes (Fig. 5e, f) in a malaria culture could be performed by Giemsa staining after microarray scanning.
cDNA synthesis, labeling, hybridization, and microarray scanning were performed by the Centre for Genomics and Bioinformatics, Bloomington, IN.
cDNA synthesis, labeling, hybridization, and microarray scanning were performed by the Centre for Genomics and Bioinformatics, Bloomington, Indiana.
Afterwards, arrays were washed and scanned by the Microarray Scanner G2505B (Agilent Technologies).
Hybridization and scanning was done by the microarray facility in the University of Pennsylvania.
The signal intensity emitted by each probe on the microarray was scanned using a GeneChip® Scanner 3000 and analyzed with Command Console Software 3.1 using the default settings.
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