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Figure 7 | BMC Bioinformatics

Figure 7

From: Data analysis issues for allele-specific expression using Illumina's GoldenGate assay

Figure 7

Intensity trends in slope and intercept for the regression analysis between the cDNA and gDNA log-ratios. The slopes and intercepts were calculated from the data in Tan et al. (2008) for SNPs with at least 3 AA and 3 BB individuals from the complete set of 142 samples. The average intensity for each SNP (calculated using the same data) is plotted on the x-axis. In total 277 SNPs are plotted from panel 1 and 261 from panel 2. Log-ratios were calculated after within-array quantile normalization of the Cy5 and Cy3 intensities. This figure shows an increasing trend for slope as average intensity increases. There is no such trend for intercept.

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