[BioC] limma reposTools problem

[Daofeng Li]

Hi Jim,

Thank you for your reply

i indeed use biocLite to install BioC,but i use the
"install.packages("affylmGUI",contriburl="http://bioinf.wehi.edu.au/affylmGUI")
" to install affylmGUI

the command you told me will update all packages i installed?
that's great!

after update sucessfully,the repos error no occured again

would you remind me ask another question?
i do Medicago GeneChip analysis by affylmGUI (six time points,no replicates)
i have medicagocdf installed
but why the output of Top 50 DE genes have no Gene Symbol?only with
ID,M and A coloum
when i try to output a html report,the DE gene part have no content
with some error:
> affylmGUI()
Searching for user-defined affylmGUI commands in
/usr/local/lib/R/library/affylmGUI/etc ...
> Loading required package: xtable
Loading required package: R2HTML
Error in get(x, envir, mode, inherits) : variable "HTMLenv" was not found
Error in get(x, envir, mode, inherits) : variable "HTMLenv" was not found
Error in get(x, envir, mode, inherits) : variable "HTMLenv" was not found
Error in get(x, envir, mode, inherits) : variable "HTMLenv" was not found
Error in get(x, envir, mode, inherits) : variable "HTMLenv" was not found
Error in get(x, envir, mode, inherits) : variable "HTMLenv" was not found
Error in get(x, envir, mode, inherits) : variable "HTMLenv" was not found

i will appreciate if anyone give me a response!
thank you!

On 6/11/07, James W. MacDonald <jmacdon at med.umich.edu> wrote:
> 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)
>
> Best,
>
> Jim
>
>
> >
> >
> >>sessionInfo()
> >
> > R version 2.5.0 (2007-04-23)
> > i686-pc-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=en_US.UTF-8;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] "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.
> Biostatistician
> Affymetrix and cDNA Microarray Core
> University of Michigan Cancer Center
> 1500 E. Medical Center Drive
> 7410 CCGC
> Ann Arbor MI 48109
> 734-647-5623
>
>
> **********************************************************
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>



-- 
Daofeng Li