Dear Bioconductor, I have installed the Category package 1.0.1 on my Windows 2000 computer, after installation of R 2.1.0 and other packages required by Category (Biobase 1.5.12; tools -- not listed in R package list; genefilter 1.6.2 actually loads 1.6.1; KEGG 1.8.1; hgu95av2 1.8.4; ALL 1.0.2; survival 2.17; splines -- no longer listed in Bioconductor package list) I would like to use the Category package for microarray data analysis. I am not an experienced R user, so I get easily confused. The Category vignette code works well until line: > Amat = t(PWAmat("hgu95av2")) where PWAmat is a function from the 'annotate' package -- not uploaded by Category and no error reported when loading the Category package. I could find a fix by loading and installing 'annotate' from local zip file. Could you make 'Category' report an error when 'annotate' is not loaded? Also could you point me to the latest 'splines' package or any other that replaces it? -- I found 'splines' yesterday morning but no longer yesterday afternoon. Then the code breaks again at line: > tA = AmER2 %*% tobs$statistic generates Error: Object "tobs" not found I suppose 'tobs' is a matrix calculated from 'ttests' described higher in the vignette, because of the matrix multiplication operator. I tried: > tA = AmER2 %*% ttests$statistic which is probably silly because it generates: Error in AmER2 %*% ttests$statistic : non-conformable arguments Could you include in the vignette the code to obtain 'tobs' and send me a copy? Thank you very much in advance for your kind help, Jean-Marc Jean-Marc Neefs, PhD Senior Bioinformatics Specialist Johnson&Johnson PRD, Janssen Pharmaceutica 30 Turnhoutseweg, B-2340 Beerse tel +32 14 60 6084 fax +32 14 60 3226 eml jneef1@prdbe.jnj.com [[alternative HTML version deleted]]

Hi Jean-Marc, You have not told us how you are getting your packages but I suspec that it is not using any of the tools provided by R. If you use install.packages (or for BioC reposTools and then install.packages2) all dependencies should be downloaded. If you choose to do this manually without using these tools, then you are going to have to sort the dependencies out yourself (and that seems to be most of what is happening here). Much of this is documented on the BioC website - I refer you there. A few more comments below. Neefs, Jean-Marc [PRDBE] wrote: > Dear Bioconductor, > > I have installed the Category package 1.0.1 on my Windows 2000 computer, > after installation of R 2.1.0 and other packages required by Category > (Biobase 1.5.12; tools -- not listed in R package list; tools is a standard R package and comes with every copy of R, if you do not have it then you did something wrong at installation time. genefilter 1.6.2 > actually loads 1.6.1; R can only load packages you downloaded. There is no magic here, if you download 1.6.1 then that is what you have. If you want 1.6.2 you must download it (or as I said above please use the tools that have been written and documented). KEGG 1.8.1; hgu95av2 1.8.4; ALL 1.0.2; survival 2.17; > splines -- no longer listed in Bioconductor package list) > splines is a package that is distributed with R. Every copy of R has a copy of splines. > packageDescription("splines") Package: splines Version: 2.1.0 Priority: base Title: Regression Spline Functions and Classes Author: Douglas M. Bates <bates@stat.wisc.edu> and William N. Venables <bill.venables@cmis.csiro.au> Maintainer: R Core Team <r-core@r-project.org> Description: Regression spline functions and classes License: GPL Version 2 or later. Built: R 2.1.0; x86_64-unknown-linux-gnu; 2005-05-10 11:52:33; unix > I would like to use the Category package for microarray data analysis. I am > not an experienced R user, so I get easily confused. > > The Category vignette code works well until line: > >>Amat = t(PWAmat("hgu95av2")) > > where PWAmat is a function from the 'annotate' package -- not uploaded by > Category and no error reported when loading the Category package. > I could find a fix by loading and installing 'annotate' from local zip file. > > Could you make 'Category' report an error when 'annotate' is not loaded? > Yes, but it would not help. Packages list only direct dependencies, other dependencies are determined by the direct dependencies. If you want to do manual installation, you are responsible for following the tree. > Also could you point me to the latest 'splines' package or any other that > replaces it? -- I found 'splines' yesterday morning but no longer yesterday > afternoon. > I have no idea what you are splines comes with R (it is a base package), you seem to have a very broken installation and can only suggest that you try to find out what has gone wrong and fix it. Best wishes Robert > Then the code breaks again at line: > >>tA = AmER2 %*% tobs$statistic > > generates Error: Object "tobs" not found > > I suppose 'tobs' is a matrix calculated from 'ttests' described higher in > the vignette, because of the matrix multiplication operator. I tried: > >>tA = AmER2 %*% ttests$statistic > > which is probably silly because it generates: Error in AmER2 %*% > ttests$statistic : non-conformable arguments > > Could you include in the vignette the code to obtain 'tobs' and send me a > copy? > > Thank you very much in advance for your kind help, > > Jean-Marc > > Jean-Marc Neefs, PhD > Senior Bioinformatics Specialist > Johnson&Johnson PRD, Janssen Pharmaceutica > 30 Turnhoutseweg, > B-2340 Beerse > > tel +32 14 60 6084 > fax +32 14 60 3226 > eml jneef1@prdbe.jnj.com > > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor >