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