[BioC] BiocLite eror

[Steve Lianoglou]

Hi,

On Wed, Apr 2, 2014 at 12:04 AM, Rabia Johnson <Rabia.Johnson at mrc.ac.za> wrote:
> 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'
>
>
> 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

Perhaps your `probeset.list$ID` isn't what you think it is?

What is the output of `head(probeset.list$ID)` ?

-steve

-- 
Steve Lianoglou
Computational Biologist
Genentech