[BioC] [Limma] annotation (probeids) and as.environment

Claudia Molina ramos.beatriz at gmail.com
Tue Dec 27 12:36:11 CET 2005


Hello and merry christmas!

I'm trying to make automatically these commands
        library(annaffy)
        library(moe430a)
        probeids <- ls(moe430aSYMBOL)
        probeids[1:2]

*If I write the below script, everything is allrigth:
        x<-moe430aSYMBOL
        is.environment(x)     #check that "x" object is an environment
           [1] TRUE
        probeids <- ls(x)    #store probe names of "moe430a" in probeids 
object

*but if  I write:
        library(annaffy)
        library(pkg, character.only = TRUE)
        x<-paste(pkg,"SYMBOL",sep="")
        is.environment(x)
          [1] FALSE
        probeids <- ls(x)

where "pkg"  is  "moe430a"

appears the next message: 
    << Error in as.environment(pos) : no item called "moe430aSYMBOL" in 
the search list >>


*I have also tried  
        probeids <- objects(paste(pkg,"SYMBOL",sep=""))
            << Error in as.environment(pos) : no item called 
"moe430aSYMBOL" in the search list >>
and
        x<-paste(pkg,"SYMBOL",sep="")
        as.environment(x)
             << Error in as.environment(x) : no item called 
"moe430aSYMBOL" in the search list >>

but they don't work and  I need all the commands are automatic  (I can't 
write "x<-moe430aSYMBOL" because my script is inside another and I won't 
know the name of the package 'a priori')

Thanks!!!

Claudia



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