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Figure 3 | BMC Genomics

Figure 3

From: The 'PUCE CAFE' Project: the First 15K Coffee Microarray, a New Tool for Discovering Candidate Genes correlated to Agronomic and Quality Traits

Figure 3

Quality Analyses between Biological and Technical Hybridization Replicates for Experiment 1 (Bean, Flower and Leaf). Hybridizations 1-6 correspond to Leaf-Bean comparisons. Hybridizations 7-12 correspond to Flower-Leaf comparisons and hybridizations, and 13-18 correspond to Bean-Flower comparisons. The box-plots allow us to compare the log2 (ratio) distribution of all the hybridizationsbefore (A) and after (B) normalization. The distribution of log2 ratios for all the comparisons is shown on one plot. The baseline is set to a similar raw expression level, allowing the inter-chips comparison. (C) Hierarchical clustering of samples using Euclidean Distance on normalization data. The samples cluster primarily by replicates. In blue is the flower-leaf comparison; in green, the leaf-bean comparison and in brown, the bean-flower comparison. (D) Person correlation at gene-level for all the probes in the replicates of the microarray. All the replicates showed a correlation value greater than p > 0.89 thus showing a high level of similarity.

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