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James Anderson wrote: > Hi, > > I am trying to use the function justMAS to normlize a bunch of Affy arrays, I loaded the library simpleaffy into R, when I type justMAS, it can not find it. > > I am not sure whether this is related to the following warning message I got: > > Loading required package: genefilter > Error in loadNamespace(i, c(lib.loc, .libPaths())) : > there is no package called 'DBI' So it looks like you have managed to not download packages according to the instructions here: http://www.bioconductor.org/download of if you did, that you did something untoward afterwards. Perhaps the best starting place is to follow that advice, eg: source("http://bioconductor.org/biocLite.R") biocLite("simpleaffy") (indeed you may be better off just reinstalling all, via biocLite() ) and then, after that, if you still have problems, perhaps you could follow the advice on the posting guide and provide the output of sessionInfo()? Robert > Error: package 'genefilter' could not be loaded > > BTW, I am using R 2.6.1, and the function mas5 functions well. > > Thanks, > > James > > > > --------------------------------- > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > -- Robert Gentleman, PhD Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M2-B876 PO Box 19024 Seattle, Washington 98109-1024 206-667-7700 rgentlem at fhcrc.org

Hi James, James Anderson wrote: > Hi, > > I am trying to use the function justMAS to normlize a bunch of Affy arrays, I loaded the library simpleaffy into R, when I type justMAS, it can not find it. > > I am not sure whether this is related to the following warning message I got: Of course it is! > > Loading required package: genefilter > Error in loadNamespace(i, c(lib.loc, .libPaths())) : > there is no package called 'DBI' > Error: package 'genefilter' could not be loaded An error is not a warning! Generally speaking, and that's true with any software, you'll find it very useful to make the distinction between an error and a warning. Roughly speaking you'll get an error when the task could not be achieved and a warning when the task could be achieved but maybe not in the way you would have expected. Even if the content of an error or warning message has sometimes an obscure meaning, it is very important to understand what kind of problem is reported: is it an error (always a serious problem, should never be ignored) or a warning (could be serious or not, needs further investigation)? Cheers, H. > > BTW, I am using R 2.6.1, and the function mas5 functions well. > > Thanks, > > James > > > > --------------------------------- > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor