Hi, I am trying to use affy package. library(affy) Data<-ReadAffy() eset<-rma(Data) Then I found the following message: Error in .;ocal(object, which, ...) : couldn't find function "multiget" And I tried to search "multiget" functions with no success. I must missed some packages from bioconductor. Could you tell me which package "multiget" belongs. BTW, I can't install bioconductor through getBioC() due to some firewall settings. So what I did is dowload each packages on my local machine, then install packages individually locally. Do i missed anythings here? And I also installed every packages "Affy" depended such as Biobase, reposTools, tkWidgets. Thanks. Nan

> I am trying to use affy package. >From 'devel' or 'release1.4'? > And I tried to search "multiget" functions with no success. I must missed some > packages from bioconductor. Could you tell me which package "multiget" > belongs. The multiget function exists in Biobase for release1.4, but will throw a warning on usage (as it was deprecated). It does not exist at all in BioC-devel (in favor of using R's 'mget()' function). > install packages individually locally. Do i missed anythings here? And I also > installed every packages "Affy" depended such as Biobase, reposTools, > tkWidgets. Again - which version of affy, Biobase, etc ... from devel or release1.4? If you encountered this problem in the release1.4 version, you definitely should let the maintainers of the affy package know about this. Actually, even if you encountered it in the devel version, you should let them know. -J

The bioconductor is from release 1.4. And the affy is version 1.5.0. Biobase_1.4.16. I definitely installed and loaded Biobase. Is this only me that get this error message? The maintainers is on this email list, right? Nan >===== Original Message From Jeff Gentry <jgentry@jimmy.harvard.edu> ===== >> I am trying to use affy package. > >From 'devel' or 'release1.4'? > >> And I tried to search "multiget" functions with no success. I must missed some >> packages from bioconductor. Could you tell me which package "multiget" >> belongs. > >The multiget function exists in Biobase for release1.4, but will throw a >warning on usage (as it was deprecated). It does not exist at all in >BioC-devel (in favor of using R's 'mget()' function). > >> install packages individually locally. Do i missed anythings here? And I also >> installed every packages "Affy" depended such as Biobase, reposTools, >> tkWidgets. > >Again - which version of affy, Biobase, etc ... from devel or release1.4? > >If you encountered this problem in the release1.4 version, you definitely >should let the maintainers of the affy package know about this. Actually, >even if you encountered it in the devel version, you should let them know. > >-J

Jeff, You are cool. Thanks very much. After using all the packages from release 4, there is no problem. Nan >===== Original Message From Jeff Gentry <jgentry@jimmy.harvard.edu> ===== >> The bioconductor is from release 1.4. And the affy is version 1.5.0. >> Biobase_1.4.16. I definitely installed and loaded Biobase. Is this only me > >The release 1.4 version of affy is '1.4.32' and the release 1.4 version of >Biobase is '1.4.15'. The current devel version of affy is '1.5.2' and >Biobase is '1.4.16'. > >So, you're definitely using the devel version of the software. I suspect >that if you updated to the latest devel affy, that this problem would go >away (I believe that they had a multiget in a slightly older version), or >if you do indeed want to use the 1.4 release versions, switch to using >those and that should also solve the problem.