[BioC] annotation of a probe in hgu133plus2

James W. MacDonald jmacdon at uw.edu
Thu Jan 9 19:11:34 CET 2014

Hi Mayte,

The gene isn't missing, instead this probeset interrogates two different 
genes. Plus you are using really old methods to get the data you want. 
These days you should use select().

 > select(hgu133plus2.db, "207356_at", c("SYMBOL","ENTREZID"))
1 207356_at DEFB4A      1673
2 207356_at DEFB4B 100289462
Warning message:
In .generateExtraRows(tab, keys, jointype) :
   'select' resulted in 1:many mapping between keys and return rows

And you get a warning saying that this probeset maps to more than one 
gene and symbol.



On 1/9/2014 12:10 PM, Mayte Suarez-Farinas wrote:
> Dear annotation builders
> I notice that one of my favorite genes DEFB4A is missing from the hgu133plus2.db
> the NetAffy database says that probeset 207356_at correspond to gene DEFB4A
> yet getSYMBOL('207356_at','hgu133plus2.db') returns NA. This happen in newer versions of
> this package, since it has been tehre before.. This gene is extremely important in
> lots skin diseases, inflammation etc, so it is a concern for my colleagues
> Any help is appreciated,
> Mayte Suarez-Farinas
> Research Assistant Professor
> Laboratory of Investigative Dermatology
> Biostatistician, Center for Clinical and Translational Science
> The Rockefeller University
> 1230 York Ave, Box 178
> New York, NY 10065
> Phone:  +1(212) 327-8213
> Fax:       +1(212) 327-8232
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James W. MacDonald, M.S.
University of Washington
Environmental and Occupational Health Sciences
4225 Roosevelt Way NE, # 100
Seattle WA 98105-6099

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