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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" Best, Jim > > 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 > > > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- James W. MacDonald, M.S. Biostatistician Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109 734-647-5623 ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues.

"James W. MacDonald" <jmacdon at="" med.umich.edu=""> writes: > 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" In the latest release of the annotate package there is a function called getAnnMap. With it, you can do: > getAnnMap("SYMBOL", "hgu95av2") <environment: 0x39c56b4=""> and so on. This function is recommended especially for scripts and package code because it provides an interface between what the objects are actually called and how you ask for them... + seth -- Seth Falcon | Computational Biology | Fred Hutchinson Cancer Research Center http://bioconductor.org