Hi Daniel, Bioconductor 2.0 is the development version. Bioconductor 1.9 is quite recent (Oct 9th to be precise), so I wouldn't expect any new capabilities for it. If you give us a bit more information as to why your data is not accepted (error message, sessionInfo() output, example code) then I think the people on the list might be able to help. I have moved this discussion to the main bioconductor mailing list. It has a wider readership of people who can help you and the bioc-devel list is mostly used for discussing bioconductor development. You might want to take a look at the bioconductor posting guide as well (http://www.bioconductor.org/docs/postingGuide.html). Following it makes our life a lot easier and means that you're much more likely to get an useful answer. hope this helps, Francois On Fri, 2006-10-27 at 19:44 -0200, Daniel Macedo Lorenzini wrote: > Dear Developing Team, > > First I would like to thank you for your effort to develop such a nice > code as Bioconductor. > > Unfortunately I have found many difficulties during the installation of > Bioconductor. I have started on Bioconductor to analyse a Nimblegen chip > dataset at probe level. Initially I worked on a Debian etch system, with > R 2.4 installed. In the current stable Bioconductor distro the Nimblegen > data is not accepted. So I tried to install the Bioconductor 2.0, which > needs R 2.5 (I don t understand why). There is no debian package for R > 2.5, so I got the R source code. R source doesn t compile because it doesn > t like my xorg installation (I do have the x11-dev package installed). So > I gave up my linux installation (shame on me) and went into the Window$ R > 2.5. I got it correctly installed, all the affy and oligo packages I > needed were download and I prepared my Nimblegen chip design library with > commands such as the following: > > > library(makePlatformDesign) > > makePDpackage("2004-11-09_Human_60mer_TEST.ndf", "ngsExpression1.xys", manufacturer="nimblegen") > > for my surprise I could not install such package with the R CMD INSTALL. > Searching some more I found that Perl and MinGW would be useful. Still > didn t make it. I find nothing else to change. > > I wonder why the Bioconductor developing team cannot work on a widely > distributed R version. After one week of work I found out that it will be > easier to come back home (linux), prepare a Perl script to fake Nimblegen > data as Affymatrix data and then work on the stable bioconductor version. > > Regards, > > Daniel Lorenzini > > _______________________________________________ > Bioc-devel at stat.math.ethz.ch mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel >