If this were going on, its effect would be most noticeable in probes that would otherwise be very dark, and appears to be present in our data, where a substantial fraction of probes that are predicted to have very low intensities appear to have much higher than expected intensity.
Still, a substantial collection of probes seem to show very low average intensity values.
Nevertheless, there is a substantial proportion of probes that are called on one platform and not on another.
However, closer examination of these correlations revealed that a substantial proportion of probes yielded very low signal intensities in cross-species hybridizations.
While a majority of probesets are perfectly mapped to the genome and annotated to one gene and a few transcripts, a substantial number of probes and probesets present some difficulties in the mapping and annotation to transcript.
Although commercial microarrays are designed to minimize the inclusion of known common sequence variants in such sites, several studies have shown that a substantial fraction of probes contain at least one SNP (31, 32).
This was due in part to the fact that approximately half of the probes used for RFLP mapping in Prunus have more than one copy [ 28, 29] and that a substantial number of probes used in T×E (30%) come from families other than the Rosaceae [ 14].
In all studies a substantial increase in regulated probe sets is seen when the MP dose is increased (data not shown).
In addition, in the course of designing selective probes, a substantial amount of structure/activity information is usually generated.
The absence of a significant background signal gives smart probes a substantial signal advantage over simple targeted agents.
When recognized and properly interpreted, VINOs recovered a substantial fraction of discarded probes and counteracted SNP ascertainment bias.
