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Afsaneh ▴ 10

@afsaneh-1755

Last seen 10.3 years ago

Hi 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 problem is env parameter. Thanks Afsaneh

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ADD COMMENT • link updated 18.5 years ago by Nianhua Li ▴ 870 • written 18.5 years ago by Afsaneh ▴ 10

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John Zhang ★ 2.9k

@john-zhang-6

Last seen 10.3 years ago

> >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 >https://stat.ethz.ch/mailman/listinfo/bioconductor >Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor Jianhua Zhang Department of Medical Oncology Dana-Farber Cancer Institute 44 Binney Street Boston, MA 02115-6084

ADD COMMENT • link 18.5 years ago John Zhang ★ 2.9k

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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 > >https://stat.ethz.ch/mailman/listinfo/bioconductor > >Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > > Jianhua Zhang > Department of Medical Oncology > Dana-Farber Cancer Institute > 44 Binney Street > Boston, MA 02115-6084 > > _______________________________________________ > 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 > -- 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 Fax: 951-827-4437

ADD REPLY • link 18.5 years ago Thomas Girke ★ 1.7k

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Nianhua Li ▴ 870

@nianhua-li-1606

Last seen 10.3 years ago

Hi, A new version (1.12.1) of ath1121501 and ag is available at http://bioconductor.org/packages/1.8/Arabidopsis_thaliana.html . It was generated by using the same source data as was used in version 1.12.0, more precisely, GeneChip annotation data downloaded from Affymetrix on Dec 18, 2005, and gene annotation data downloaded from TAIR on March 19, 2006. The new version has a new environment called ath1121501GENENAME (and agGENENAME). The data source of it was ftp://ftp.arabidopsis.org/home/tair/Genes/TAIR_sequenced_genes . Hope it will be helpful for Afsaneh. We only have unix/linx and windows version available, and the OS X version will be there in about a week. thanks Nianhua Li Computational Biology, PHS, FHCRC

ADD COMMENT • link 18.5 years ago Nianhua Li ▴ 870

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Stephen Henderson ★ 1.0k

@stephen-henderson-71

Last seen 7.7 years ago

If it's similar to other anno packages then it will be "Ath1121501GENENAMES" with an S on the end. Stephen Henderson Wolfson Inst. for Biomedical Research Cruciform Bldg., Gower Street University College London United Kingdom, WC1E 6BT +44 (0)207 679 6827 -----Original Message----- From: bioconductor-bounces@stat.math.ethz.ch [mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of Afsaneh Sent: 12 June 2006 14:51 To: bioconductor at stat.math.ethz.ch Subject: [BioC] environment Hi 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 problem is env parameter. Thanks Afsaneh _______________________________________________ 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 ********************************************************************** This email and any files transmitted with it are confidentia...{{dropped}}

ADD COMMENT • link 18.5 years ago Stephen Henderson ★ 1.0k

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