Querying PubMed Database
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@christina-kendziorski-452
Last seen 7.7 years ago
I am very interested to query PubMed using Bioconductor. I can load annotate, affy, affydata without trouble. I've run RMA on data sets without problems. For some reason, I am running into trouble when trying to follow the instructions in "HowTo:Automated Querying of PubMed Data". I can't load hgu95av2. That library is "not found". > library(hgu95av2) Error in library(hgu95av2) : There is no package called 'hgu95av2' Since this is the case, I downloaded it from Bioconductor and installed it in my working directory using R CMD INSTALL -l "." hgu95av2_1.3.1.tar.gz It seemed to install just fine, but when I try to read it into R using library(hgu95av2, lib.loc=".") and various permutations of that command, the library is still not found. I tried to get around this by sourcing in the hgu95av2 file that is in local/hgu95av2/R...This did not work either. Any suggestions ? I should note that I am actually interested in rae230a chips and so I first tried everything stated above using the rae230a library. Same trouble. Because of that, I thought I would try the hgu95av2 to see if I could get it working as it is the library explicitly listed in the write up aforementioned. It didn't work. Finally, I noticed back in August that there was some problem with rae230a and b files that was going to be fixed. Was that ever done ? Thanks for any help! Christina Kendziorski Christina Kendziorski Assistant Professor Department of Biostatistics and Medical Informatics University of Wisconsin - Madison Medical Sciences Center (6729) 1300 University Avenue Madison, Wisconsin 53706 Phone: (608) 262-3146 Fax: (608) 265-7916
hgu95av2 rae230a annotate affy affydata hgu95av2 rae230a annotate affy affydata • 652 views
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@vincent-j-carey-jr-4
Last seen 10 days ago
United States
> > > I am very interested to query PubMed using Bioconductor. > I can load annotate, affy, affydata without trouble. > I've run RMA on data sets without problems. For some > reason, I am running into trouble when trying to > follow the instructions in "HowTo:Automated Querying > of PubMed Data". > > I can't load hgu95av2. That library is "not found". > > > library(hgu95av2) > Error in library(hgu95av2) : There is no package called 'hgu95av2' > > > Since this is the case, I downloaded it from Bioconductor > and installed it in my working directory using > > R CMD INSTALL -l "." hgu95av2_1.3.1.tar.gz what operating system are you using? presumably a *nix. what version of R? > > It seemed to install just fine, but when I try to read it > into R using library(hgu95av2, lib.loc=".") and various > permutations of that command, the library is still not found. > I tried to get around this by sourcing in the hgu95av2 file > that is in local/hgu95av2/R...This did not work either. but if you installed it in ".", why would you look in "local/hgu95av2"? where is the 'local' coming from? > Any suggestions ? never try to install R package resources except by the R package handling mechanisms, unless you are very sure of what you are doing. you could use reposTools and install.packages2, or you can obtain the tar.gz file and run the install command appropriately. since it appears that you do not have write access to the central R library (because you are using INSTALL -l) you may want to talk to your administrators about having them install the bioconductor resources for central use. if you do run your own version of R, install.packages2 is the easiest way to get new packages installed.
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