- Course overview
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- Introduction
- Real-time PCR
- What is Next Generation DNA Sequencing?
- RNA sequencing
- Biological interpretation of gene expression data
- Genotyping, epigenetic and DNA/RNA-protein interaction methods
- DNA/RNA-protein interactions
- Summary
- Quiz: Check your learning
- Your feedback
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- References
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Quality control
In Expression Atlas, quality control of data from all microarray technologies (Affymetrix, Agilent and Illumina) is done using the ‘arrayQualityMetrics’ R package.
Quality control of microarray data begins with the visual inspection of the scanned microarray images to make sure that there are no obvious splotches, scratches or blank areas (4).
After feature extraction, the data analysis software packages can be used to make diagnostic plots (for example of background signal, average intensity values and percentage of genes above background) to help identify problematic arrays, reporters or samples (Figure 6).
