for the archives: updating to the latest pdInfoBuilder solved the problem. b On Fri, Feb 5, 2010 at 2:00 PM, Benilton Carvalho <beniltoncarvalho at="" gmail.com=""> wrote: > The current version of the pdInfoBuilder package is 1.10.0. > > So, my first recommendation is to upgrade your R installation to the > latest available version, so you can use the aforementioned > pdInfoBuilder package. > > Once that's done, I'd suggest you to try the script again and I'll be > able to help you out. > > Cheers, > > b > > On Fri, Feb 5, 2010 at 1:52 PM, Chris Fenton <chrisf at="" fagmed.uit.no=""> wrote: >> Pretty much copied the code from >> http://linusben.net/wiki/index.php/Oligo.bioconductor. >> >> >> Something ala, >> >> """ >>> library(pdInfoBuilder) >>> filename_ndf <- list.files('.',pattern='.ndf',full.names=T) >>> filename_xys <- list.files('.',pattern=".xys",full.names=T)[1] >>> seed <- new("NgsExpressionPDInfoPkgSeed", ndfFile=filename_ndf, xysFile=filename_xys, >> ? ? ? ? ? ?author="Taejoon Kwon",email="email address", >> ? ? ? ? ? ?biocViews="AnnotationData", genomebuild="Unknown", >> ? ? ? ? ? ?url="http://www.marcottelab.org") >>> makePdInfoPackage(seed, destDir = ".") >> """ >> >> I get the folling error in the seed <- new(...) line >> >> """ >> argument "posFile" is missing, with no default >> """ >> >> >> Can't seem to find any documentation on this parameter. >> Anyone run into this ? >> >> Chris >> >> >> >> sessionInfo() >> >> R version 2.7.2 (2008-08-25) >> i686-pc-linux-gnu >> >> locale: >> C >> >> attached base packages: >> [1] splines ? tools ? ? stats ? ? graphics ?grDevices utils ? ? datasets >> [8] methods ? base >> >> other attached packages: >> [1] pdInfoBuilder_1.4.0 ?oligo_1.4.0 ? ? ? ? ?oligoClasses_1.2.0 >> [4] AnnotationDbi_1.2.2 ?preprocessCore_1.2.1 affxparser_1.12.2 >> [7] RSQLite_0.7-1 ? ? ? ?DBI_0.2-4 ? ? ? ? ? ?Biobase_2.0.1 >> >> _______________________________________________ >> 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 >> >