Annotation package for Agilent Human G4110A chip
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Tim Smith ★ 1.1k
@tim-smith-1532
Last seen 7.1 years ago

Hi,

I couldn't find the G4110A chip in the annotation packages that can be downloaded from bioconductor. Does anyone know if I will be able to use some other annotation package for this chip?

Tim 

 

Agilent annotation • 923 views
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Marc Carlson ★ 7.2k
@marc-carlson-2264
Last seen 5.1 years ago
United States

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

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Tim Smith ★ 1.1k
@tim-smith-1532
Last seen 7.1 years ago

Thanks Marc, that worked!

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