[BioC] Annotation package for Agilent Human G4110A chip

[Marc Carlson]

Tim Smith wrote:
> Hi,
>
> I couldn't find the G4110A chip in the annotation packages that cann be downloaded from bioconductor. Does anyone know if I will be able to use some other annotation package for this chip?
>
> Tim 
>
>
>
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Hi Tim,

According to Agilent the G4110A and G4110B parts were both variants of
the Human 1A version 2 platform.

http://www.chem.agilent.com/Scripts/Generic.ASP?lPage=55790&indcol=N&prodcol=N


And according to records at NCBI:

http://www.ncbi.nlm.nih.gov/projects/geo/query/acc.cgi?acc=GPL885

http://www.ncbi.nlm.nih.gov/projects/geo/query/acc.cgi?acc=GPL887

The G4110B variant of that series of Agilent chips has about 3K more
probes on it.  If we assume that the biggest difference between the A
and B variants of theses two chips is that they mostly added probes to
the newer version rather than dropping them (pretty likely), and also
assume that Agilent does not recycle their probe IDs (this is extremely
likely, but you still have to verify it with Agilent since it is a
critical detail for this to mean anything) then the annotation package
we already make for the later "B" version of that chip will probably get
you most of the information that you want for that "A" version as well. 
This package is called:

hgug4110b.db


Alternatively, you can often just get what you need from an organism
based annotation.  In your case this package:

org.Hs.eg.db

Should provide most things that you might want for humans (in an entrez
gene centric fashion).

If neither of these options is adequate, then you can always make a new
Annotation package from scratch by using AnnBuilder or you can even try
out the newest  SQLforge code from the AnnotationDbi package (presently
this still requires the development version of things) to make more
modern ".db" style Annotation packages.


I hope this helps,


    Marc