Probe mapping file

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To generate Land views from Array data, ALV files are generated from Analysis projects. For Agilent and Affymetrix expression arrays (in which a probe(s) are assigned to genes in the annotation file from the vendor), these arrays need to incorporate genomic positioning. This is done by mapping the probe sequence files to the genome and gene models used for generating the Land. The mapping function is explained here: Probe Mapping File. This mapping will be to specific genomic coordinates (not to individual genes). Within the Land created, probes with any overlap with a given gene from this mapping will be assigned to all such genes. Therefore, users may notice that probes that were annotated by Agilent/Affymetrix do not completely share the same ProbeID to GeneID mapping.

Example: In the genome browser below, we can see two probes (Arrows) map to two genes in the Human genome. Since there is a overlap of each probe with the neighboring gene, both genes will be called for both genes in Land view. In the original annotation file for these probes, only the gene with the best match was called: