[BioC] specifying metadata packages on the fly

James W. MacDonald jmacdon at med.umich.edu
Wed Jun 13 20:53:11 CEST 2007

Hi Tae-Hoon,

Tae-Hoon Chung wrote:
> Hi, All;
> I have some probe ids say in HG-U133 Plus2 chips and I want to  
> retrieve the gene names attached to them. This can be done like get 
> ('239651_at', hgu133plus2SYMBOL). But when I tried get('239651_at',  
> paste('hgu133plus2', 'SYMBOL', sep='')), this one failed. Is there  
> any way I can make the latter approach work? The thing is I know the  
> package is 'hgu133plus2' but, depending on the situation, I want to  
> use different suffixes such as 'SYMBOL', 'ACCNUM', 'ENTREZID'  
> interchangeably. Thanks in advance!

You are missing a get() statement. Note the following:

 > library(hgu133plus2)
 > paste("hgu133plus2", "SYMBOL", sep="")
[1] "hgu133plus2SYMBOL"
 > get(paste("hgu133plus2", "SYMBOL", sep=""))
<environment: 0x0178922c>
 > get("1007_s_at", get(paste("hgu133plus2", "SYMBOL", sep="")))
[1] "DDR1"



> Tae-Hoon Chung
> Post-Doctoral Researcher
> Computational Biology Division, TGEN
> 445 N 5th St. Phoenix, AZ 85004 USA
> O: 1-602-343-8724
> F: 1-602-343-8840
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James W. MacDonald, M.S.
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109

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