Figure 1.

Illustration of the two types of multi-match probes. (A) One probe shares a subsequence with two separate transcribed regions. Such a probe would belong to two probesets—one targeting each region. (B) Probes under the leftmost exon capture signal from isoform 1, while the other probes capture signal from isoforms 1 and 2. In order to estimate expression at the isoform level, probes should be grouped into two probesets—one targeting each isoform. If both isoforms are present in the sample, the probe signal will tend to be higher at the multi-match probes than at the single-match probes.