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Figure 3 | BMC Plant Biology

Figure 3

From: Transcript profiling of common bean (Phaseolus vulgaris L.) using the GeneChip®Soybean Genome Array: optimizing analysis by masking biased probes

Figure 3

Selection of the optimum signal intensity threshold for masking probes targeting interspecies-variable regions. A. The number of probes (triangles) and probe sets (circles) retained after masking probes with a series of signal intensity thresholds. B. Effect of probe masking over a range of signal intensity thresholds (0-640) on the number of probe sets commonly-selected in soybean and common bean (circles) and the correlation of the Leaf/Nodule hybridization intensity ratio for the commonly selected genes (triangles). A signal intensity threshold of 80 (red star) was selected to mask biased probes. Commonly-selected genes are defined as genes exhibiting at least a 2-fold difference in hybridization intensity expression ratio between leaf and nodule tissue (leaf vs. nodule, ≥ 2-fold difference) for both soybean and common bean.

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BMC Plant Biology

ISSN: 1471-2229

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