[BioC] Does the strand of a microarray probe matter?

[Cei Abreu-Goodger]

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?

# 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