[BioC] BiocLite eror

[Dan Tenenbaum]

----- Original Message -----
> From: "Rabia Johnson" <Rabia.Johnson at mrc.ac.za>
> To: bioconductor at r-project.org
> Sent: Wednesday, April 2, 2014 12:04:19 AM
> Subject: [BioC] BiocLite eror
> 
> HI,
> 
> Object : problem with hgu133plus2.db  you need to install this
> package to complete this step
> 
> If possible can anyone help. I am new to R and are working through
> the tutorial of Daniel Swan (Analysing microarray data in
> BioConductor)
> Upon writing the following command I get the following error:
> 
> > biocLite("hgu133plus2.db")
> BioC_mirror: http://bioconductor.org
> Using Bioconductor version 2.13 (BiocInstaller 1.12.0), R version
> 3.0.3.
> Installing package(s) 'hgu133plus2.db'
> Warning: package 'hgu133plus2.db' is in use and will not be installed
> Warning message:
> installed directory not writable, cannot update packages 'boot',
> 'class',
>   'cluster', 'foreign', 'KernSmooth', 'MASS', 'Matrix', 'mgcv',
>   'nlme', 'nnet',
>   'rpart', 'spatial'
> 
> 

Try quitting your R session and starting a fresh one like this:

R --vanilla

And then running


source("http://bioconductor.org/biocLite.R")
biocLite("hgu133plus2.db")


Does that work?

Dan



> Thus, needless to say when I continue with the next command I get
> more errors:
> 
> > library(hgu133plus2.db)
> > library(annotate)
> > gene.symbols <- getSYMBOL(probeset.list$ID, "hgu133plus2")
> Error in unlist(lookUp(x, data, "SYMBOL")) :
>   error in evaluating the argument 'x' in selecting a method for
>   function 'unlist': Error in lookUp(x, data, "SYMBOL") : No keys
>   provided
> 
> 
> Can anyone help please
> Regards
> Rabia
> 
> 
> _______________________________________
> Rabia Johnson (PhD)
> Senior Scientist
> South African Medical Research Council
> Diabetes Discovery Platform
> Building E
> Francie van Zijl Drive, Parow Valley, 7505, Cape Town
> Cell: +27 82 0677296
> Tel: +27 21 938 0866
> Fax: +27 21 938 0456
> E-mail: rabia.johnson at mrc.ac.za
> 
> 
> Disclaimer\ \ The information contained in this
> communic...{{dropped:20}}
> 
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at r-project.org
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives:
> http://news.gmane.org/gmane.science.biology.informatics.conductor
>