[BioC] limma reposTools problem

James W. MacDonald jmacdon at med.umich.edu
Mon Jun 11 15:30:30 CEST 2007

Hi Daofeng,

Daofeng Li wrote:
> Hi list,
> i am using limma to analysis my data
> i encountered an error when using affylmGUI,it says "no reposTools"
> i search the list found Jim said reposTools was deprected
> i would like to know how to fix the "no reposTools" problem?
> Thanks for any response!
> i am using CentOS 4.4
> here comes my session info:

You have quite the mix-n-match of versions here. That version of 
affylmGUI is quite old (current is 1.10.2), so it shouldn't be 
surprising that it doesn't work.

This has been said on this list about a gazillion times, but here it is 
again. When installing Bioconductor packages your best bet is to use 
biocLite(), which will get the appropriate version of the package given 
the version of R you are using.

Another alternative is to update Biobase using biocLite(), then do 
something like this:

repos <- biocReposList()
update.packages(repos=repos, ask=FALSE)



> R version 2.5.0 (2007-04-23)
> i686-pc-linux-gnu
> locale:
> attached base packages:
>  [1] "tcltk"     "splines"   "tools"     "stats"     "graphics"  "grDevices"
>  [7] "utils"     "datasets"  "methods"   "base"
> other attached packages:
>   affylmGUI       limma     affyPLM       gcrma matchprobes    affydata
>     "1.5.4"    "2.10.0"    "1.12.0"     "2.8.0"     "1.8.1"    "1.11.2"
>        affy      affyio     Biobase
>    "1.14.0"     "1.4.0"    "1.14.0"

James W. MacDonald, M.S.
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109

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