[BioC] Re: location in chromosome

[Vincent Carey 525-2265]

> Hello,
> I would like to map some probes to their chromosome location. I am using
> the Affimetrix mu74a chip, so I have the Affimetrix call names like
> 100981_at, 93026_at, 101898_s_at, 97564_f_at, 98790_s_at, etc.
> now I would like to know in which chromosome they are and at which
> distance from the centromere.

Previous replies to this emphasized the annotate/chromLocation
structures that work for various organisms.

If you work through the byChroms vignette in geneplotter
substituting the mgu74av2 package for hu6800, you will
get the resources that answer this question.

at a lower level, it may be worth mentioning that
package mgu74av2 has environments mgu74av2CHRLOC
and mgu74av2CHR which map from the probeset names
noted above (100981_at etc) to oriented nucleotide counts
and chromosome numbers respectively

all the chip-targeted metadata resources should have
these *CHRLOC and *CHR environments that can be
queried for this sort of information.

> Is this possible with the bioconductor package?
> Thanks
> H.Ghezzo
> Meakins-Christie Labs
> Montreal - Canada
>
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