Find correct annotation for specific agilent platforms Whole Human Genome Microarray 4x44K
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@konstantinos-yeles-8961
Last seen 6 weeks ago
University of Salerno, Salerno, Italy

Dear Bioconductor Community,

I'm A newbie  in R/Bioconductor and as i have recently downloaded from GEO some Agilent data-sets with annotation Whole Human Genome Microarray 4x44K G4112F & Whole Human Genome Microarray 4x44K v2. Thus, i wonder how i could annotate my probe-sets to gene symbols. Thus, i would like to ask after searching for annotation packages, i only ended to find the most "relative" package hgug4112a.db (http://bioconductor.org/packages/release/data/annotation/html/hgug4112a.db.html)-(Agilent "Human Genome, Whole" annotation data-chip hgug4112a). So, because i don't have any kind of relative experience, is it "safe" to use the current database, or this specific annotation is irrelevant and  there are other more appropriate ways of querying my specific annotations ?

Please excuse me for my naive question, but because i realize that annotation packages for Agilent are a bit complicated to search, any help or suggestion would be essential !!

Best,

Konstantinos

agilent whole Human Genome Microarray 4X44K annotationdbi bioconductor • 2.8k views
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Axel Klenk ▴ 980
@axel-klenk-3224
Last seen 11 hours ago
Switzerland

Dear Konstantinos,

you should use hgug4112a.db for the G4112F arrays -- the genes on the arrays

are the same, only array layouts and controls are different. For the 4x44K v2

(Agilent design ID 026652, part number G4845A :-)) there is an annotation package

HsAgilentDesign026652.db.

Cheers,

 - axel

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@konstantinos-yeles-8961
Last seen 6 weeks ago
University of Salerno, Salerno, Italy

Dear Axel, thank you very much for your explanation.

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