[BioC] annotation of a probe in hgu133plus2

[James W. MacDonald]

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"))
     PROBEID 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.

Best,

Jim

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.
Biostatistician
University of Washington
Environmental and Occupational Health Sciences
4225 Roosevelt Way NE, # 100
Seattle WA 98105-6099