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Figure 1 | BMC Bioinformatics

Figure 1

From: The impact of quantitative optimization of hybridization conditions on gene expression analysis

Figure 1

Simulation study of cross-hybridization effects. To examine the impact of cross-hybridization, we considered 100 genes each with zero, low, medium, or high differential expression (Z/L/M/H). The effects of cross-hybridization were tested by adding a small off set to half of the genes in the channel with lower expression values. The likelihood, Eq. (5), is shown relative to the non-contaminated case ('no xhyb') as a baseline. From a selective perturbation of individual gene groups ('xhyb Z', 'xhyb L', 'xhyb M', 'xhyb H') we could see that cross-hybridization to probes for non-expressed genes can inflate the objective function. On the other hand, the corresponding loss for genes with medium and high expression levels is considerably larger. The overall effect of cross-hybridization for biological samples which do not show a strong bias towards either down- or up-regulation is labelled 'xhyb unbiased'. The obtained degraded likelihood shows that, as required, cross-hybridization in general has a deleterious outcome as long as unsuitably biased biological samples are avoided.

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