[BioC] environment

Thomas Girke thomas.girke at ucr.edu
Tue Jun 13 20:00:06 CEST 2006


Below is a work around for this limitation by importing the latest
annotations from the TAIR ftp site and querying the resulting 
data frame:

# Online import
ATdesc <- read.delim("ftp://ftp.arabidopsis.org/home/tair/Microarrays/Affymetrix/affy_ATH1_array_elements-2006-04-05.txt",
		 na.strings = "", fill=TRUE, header=T, sep="\t")

# Retrieving the relevant columns
ATdesc <- ATdesc[,c(1,5,6)] 

# Example for retrieving the descriptions for the AffyIDs: 253031_at and 253032_at
myquery <- c("253031_at", "253032_at")
ATdesc[ATdesc[,1] %in% myquery, ]


Thomas

On Tue 06/13/06 12:05, John Zhang wrote:
> 
> >
> >I am trying to use R for Arabidopsis data ,  but I can't get the  genes 
> >annotation  correctly, I am using  :
> >
> >mget(AffyID[1:10], env = ath1121501GENENAME)
> >Error in mget(AffyID[1:10], env = ath1121501GENENAME) :
> >        object "ath1121501GENENAME" not found
> >
> 
> 
> If you do ath1121501() you will see ath1121501GENENAME is not one of the 
> environments contained by the package.
> 
> 
> >
> >
> >problem is env parameter.
> >Thanks
> >Afsaneh
> >
> >_______________________________________________
> >Bioconductor mailing list
> >Bioconductor at stat.math.ethz.ch
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> 
> Jianhua Zhang
> Department of Medical Oncology
> Dana-Farber Cancer Institute
> 44 Binney Street
> Boston, MA 02115-6084
> 
> _______________________________________________
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> 

-- 
Thomas Girke, Ph.D.
1008 Noel T. Keen Hall
Center for Plant Cell Biology (CEPCEB)
University of California
Riverside, CA 92521

E-mail: thomas.girke at ucr.edu
Website: http://faculty.ucr.edu/~tgirke
Ph: 951-827-2469
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