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

[Claudia Molina]

Thanks!!!! it works!!!!
Thank you thank you

Claudia



Ting-Yuan Liu wrote:

>Hi Claudia,
>
>Try this:
>         library(annaffy)
>         library(pkg, character.only = TRUE)
>         x<-paste(pkg,"SYMBOL",sep="")
>         y <- get(x)
>         is.environment(y)
>           [1] TRUE
>         probeids <- ls(y)
>
>HTH,
>Ting-Yuan
>
>______________________________________
>Ting-Yuan Liu
>Program in Computational Biology
>Division of Public Health Sciences
>Fred Hutchinson Cancer Research Center
>Seattle, WA, USA
>______________________________________
>
>On Tue, 27 Dec 2005, Claudia Molina wrote:
>
>  
>
>>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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>>Bioconductor at stat.math.ethz.ch
>>https://stat.ethz.ch/mailman/listinfo/bioconductor
>>
>>    
>>
>
>  
>