On Fri, Nov 28, 2008 at 4:44 AM, Cei Abreu-Goodger <cei@ebi.ac.uk> wrote:

> Dear list,
>
> Thank you all for your answers, from these and some offline conversations I
> had with people from the microarray facility, I can see that current
> microarray protocols attempt to produce strand specific samples before
> hybridizing (but see the ref. Wolfgang sent).
>
> In this case, whenever doing probe mapping we have to be careful to select
> only those probes with sequence matching on the appropriate strand (and this
> will depend on the platform, since some manufacturers report the probe
> sequence, and some the "target" sequence). As I mentioned before, this has
> historically not always been the case.
>
> One last point, regarding one of Sean's answers:
>
> "
> There is no attempt to map probes in bioconductor annotation packages (at
> least those maintained by the core).  The annotation from which the
> annotation packages are derived come directly from the manufacturers,
> generally.
> "
>
> Even if no re-mapping is being done (there are many bioC packages not
> maintained by the core which do involve re-mapping), my main point was that
> bioconductor annotation structures don't allow more than one "gene" to be
> annotated for any particular probe. Do correct me if I'm wrong, but at least
> when using AnnotationDbi I found no way of having more than one gene
> (EntrezID) per probe.
>
> Another example: Affymetrix does annotate more than one gene (EntrezID) for
> their probes (~5% of probes in mouse430_2 with EntrezID have more than one).
> So, I guess if the bioconductor core team is using the manufacturer's
> annotation, then they are (in some way) removing this information?
>

I think the annotation is done by mapping the genbank or refseq ids to
entrez id.  The Entrez IDs from the manufacturer are not used directly, I do
not think.  However, Marc Carlson is the best to comment on the details.

Sean


>
> # bit of R code showing this:
> library(mouse4302.db)
> xx <- as.list(mouse4302ENTREZID)
> any(lapply(xx, length) > 1)
> #[1] FALSE
>
> And no, I'm not saying that different EntrezID's are always unrelated
> genes, or that multiple probes mapping to multiple genes are always due to
> strand problems.
>
> Thanks again,
>
> Cei
>
>
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