[BioC] annotation information about ecoli2
Minwook Kim
labohemekim at yahoo.com
Thu Nov 6 15:35:56 CET 2008
Hi,
I run the aafTableAnn() to get the annotation information of eocli2.
But I got the error. I did try to get the ecoli package. but it failed. Anyone help me?
> AnnTable2 <- aafTableAnn(AllGenes,chiptype,AnnCols[2]);
Loading required package: ecoli2
Error in aaf.handler(chip = chip) : Couldn't load data package ecoli2
In addition: Warning message:
In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, :
there is no package called 'ecoli2'
Apparently, the following information are helpful to fix it.
> chiptype
[1] "ecoli2"
"AllGenes" variable includes probe ids.
I guess "ecoli2" microarry is not supported by annaffy package. or I don"t know how to download the ecoli2 package.
Thanks.
Minwook
> sessionInfo()
R version 2.7.0 (2008-04-22)
x86_64-redhat-linux-gnu
locale:
LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C
attached base packages:
[1] splines tools stats graphics grDevices utils datasets
[8] methods base
other attached packages:
[1] gplots_2.6.0 gdata_2.4.2 gtools_2.5.0
[4] simpleaffy_2.16.1 ecoli2probe_2.2.0 ecoli2cdf_2.2.0
[7] bioDist_1.12.0 genefilter_1.20.1 survival_2.34-1
[10] annaffy_1.12.1 KEGG.db_2.2.0 GO.db_2.2.0
[13] AnnotationDbi_1.2.2 RSQLite_0.7-1 DBI_0.2-4
[16] gcrma_2.12.1 matchprobes_1.12.1 affy_1.18.2
[19] preprocessCore_1.2.1 affyio_1.8.1 Biobase_2.0.1
loaded via a namespace (and not attached):
[1] annotate_1.18.0
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