Madison 20 June 2008 In order to test the "oligo" package I have tried to follow the R method in the following document by Benilton Carvalho http://www.bioconductor.org/workshops/2007/BioC2007/labs/oligo/BioC200 7-oligo.pdf After many attempts it is time to write. First of, Nimblegen does not by default provide the XYS file, but they can be special-ordered (as I found from others postings). Even with the test-run data called extdata from library(maqcExpression4plex) there is still something missing and that's the package pd.hg18.60mer.expr_1.1.1 as shown in the error: > maqc <- read.xysfiles(xys.files) Loading required package: pd.hg18.60mer.expr Error in read.xysfiles(xys.files) : Must install the pd.hg18.60mer.expr package. In addition: Warning message: In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, : there is no package called 'pd.hg18.60mer.expr' > I obtain the same error if I try to load other XYS files from another source: > DATA <- read.xysfiles(xys.files) Loading required package: pd.hg18.60mer.expr Error in read.xysfiles(xys.files) : Must install the pd.hg18.60mer.expr package. Searching with Google, the only document that ever mention this package is the PDF file of the tutorial (in the last slide after the > sessionInfo() command.... I looked within the Bioconductor lists of 2.3, 2.2, 2.1., 2.0, 1.9 at which point there is no more package starting with pd.xxx I also did a search on Nimblegen analysis in Google and essentially did not find anything else useful for R. My question is this: is this package available "somewhere?" but from Google results on pd.hg18.60mer.expr_1.1.1, pd.hg18.60mer.expr and pd.hg18.60mer the ONLY document that has this string of character is the PDF tutorial... A corollary question: is there a way to do a similar analysis without the XYS file using the .pair or other standard files provided by Nimblegen? Thank you for any hint you might provide... perhaps I am not the only one wondering! Jean-Yves Sgro ------------------------------------------------ Jean-Yves Sgro, Ph.D., Senior Scientist http://myprofile.cos.com/sgroj65 ------------------------------------------------ University of Wisconsin Biotechnology Center Gene Expression Center 425 Henry Mall Madison Wi 53706 USA http://www.biotech.wisc.edu/ServicesResearch/Gec/ Fax: 608-262-6748 ------------------------------------------------ & Institute for Molecular Virology 1525 Linden Drive Madison WI 53706 tel: 608-262-7464 http://virology.wisc.edu/virusworld ------------------------------------------------ P.S. Here is the sessionInfo() from the Windows version I have tried to do this in: after the following library commands from http://www.bi oconductor.org/workshops/2007/BioC2007/labs/oligo/BioC2007-oligo.R library(oligo) library(maqcExpression4plex) library(genefilter) library(geneplotter) library(limma) library(RColorBrewer) palette(brewer.pal(8, "Dark2")) > sessionInfo() R version 2.7.0 (2008-04-22) i386-pc-mingw32 locale: LC_COLLATE=English_United States.1252;LC_CTYPE=English_United States.1252;LC_MONETARY=English_United States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252 attached base packages: [1] splines tools stats graphics grDevices utils datasets methods base other attached packages: [1] maqcExpression4plex_1.2 oligo_1.4.0 oligoClasses_1.2.0 affxparser_1.12.2 [5] preprocessCore_1.2.0 RColorBrewer_1.0-2 limma_2.14.4 geneplotter_1.18.0 [9] annotate_1.18.0 xtable_1.5-2 AnnotationDbi_1.2.1 RSQLite_0.6-8 [13] DBI_0.2-4 lattice_0.17-6 genefilter_1.20.0 survival_2.34-1 [17] Biobase_2.0.1 loaded via a namespace (and not attached): [1] grid_2.7.0 KernSmooth_2.22-22 >