Hii All,
i am facing a problem in which the datasets for certain bacteria are empty.
Can anyone please suggest what might be going wrong or is it something to
do with my commands in R(which i have tried to rule out by using the same
syntax for other datasets).
I am getting the following output.
""""
I. For e.coli its fine!
> ecoli<- useMart("bacteria_mart_14",dataset="esc_18_gene")
> check<-getBM(attribute=c("strand"),mart=ecoli)
> check
strand
1 -1
2 1
II. For B. anthracis Ames ancestor, its giving empty datasets
> gbaa<-useMart("bacteria_mart_14",dataset="bac_20000_gene")
> check<-getBM(attribute=c("strand"),mart=gbaa)
> check
[1] strand
<0 rows> (or 0-length row.names)
III my session info
> sessionInfo()
R version 2.13.2 (2011-09-30)
Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)
locale:
[1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] biomaRt_2.8.1 SpeCond_1.6.0 RColorBrewer_1.0-5 hwriter_1.3
fields_6.6.2 spam_0.27-0
[7] Biobase_2.12.2 mclust_3.4.11
loaded via a namespace (and not attached):
[1] RCurl_1.8-0 tools_2.13.2 XML_3.6-2
Can anyone please help
Regards
gurudutta
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