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_U
S.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
**********************************************************
Electronic Mail is not secure, may not be read every day, and should
not be used for urgent or sensitive issues.
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/af
fylmGUI")
" 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=e
n_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.U
TF-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
>
>
> **********************************************************
> Electronic Mail is not secure, may not be read every day, and should
not be used for urgent or sensitive issues.
>
--
Daofeng Li