Why does oligo::getProbeInfo() give a lower number of probes than the actual number of probes on Affymetrix Human Gene 1.0 ST Array ?
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8 months ago
cg1440 ▴ 30

The output of exprs(raw_data) (raw_data being the GeneFeatureSet object) has 1,102,500 entries (individual probes)

However, the output of getProbeInfo(raw_data, target = "core") has 861,493 entries. And from what I understood about this function is that it maps each individual probe to its corresponding probeset (or transcript cluster in this case i guess) (i.e. PROBEID). If that's true, why this discrepancy in the numbers? Is it that ~300k probes are not part of probesets? If not, what do these 300k probes represent?

R affymetrix oligo • 259 views

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