Hi Vincent, thanks for your reply. Here you have the sessionInfo() > sessionInfo() R version 2.13.0 Patched (2011-04-21 r55576) Platform: i386-pc-mingw32/i386 (32-bit) locale: [1] 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] stats graphics grDevices datasets utils methods base other attached packages: [1] hgu95av2cdf_2.8.0 affydata_1.11.11 affyQCReport_1.30.0 lattice_0.19-26 affy_1.30.0 Biobase_2.12.1 rcom_2.2-3.1 rscproxy_1.3-1 loaded via a namespace (and not attached): [1] affyio_1.20.0 affyPLM_1.28.5 annotate_1.30.0 AnnotationDbi_1.14.1 Biostrings_2.20.0 Cairo_1.4-9 cluster_1.13.3 DBI_0.2-5 gcrma_2.24.1 [10] genefilter_1.34.0 grid_2.13.0 Hmisc_3.8-3 hwriter_1.3 IRanges_1.10.0 latticeExtra_0.6-14 preprocessCore_1.14.0 RColorBrewer_1.0-2 RSQLite_0.9-4 [19] setRNG_2009.11-1 simpleaffy_2.28.0 splines_2.13.0 survival_2.36-9 tools_2.13.0 xtable_1.5-6 By the way, when I use the affyQCreport for a quality check the empirical density for the log intensity is plotted nicely. Maybe it helps to know that my R installation is from a bundle named RAndFriends (http://rcom.univie.ac.at/) which include a COM server to comunicate with applications like Excel and Matlab. I look forward to hear from you. Omar On Wed, May 4, 2011 at 6:45 PM, Vincent Carey <stvjc@channing.harvard.edu>wrote: > what is your sessionInfo()? > > On Wed, May 4, 2011 at 7:39 AM, Omar Gutierrez Arenas < > tardebut@gmail.com> wrote: > >> Dear Colleagues, >> >> I have been trying to run some of the examples described in the affy prime >> vignette and I'm having problems with image() and hist(). >> >> For example, >> >> > require(affy) >> >> > require(affydata) >> >> > data(Dilution) >> >> > Dilution >> trying URL ' >> >> http://bioconductor.org/packages/2.8/data/annotation/bin/windows/co ntrib/2.13/hgu95av2cdf_2.8.0.zip >> ' >> Content type 'application/zip' length 1343719 bytes (1.3 Mb) >> opened URL >> downloaded 1.3 Mb >> package 'hgu95av2cdf' successfully unpacked and MD5 sums checked >> The downloaded packages are in >> C:\Users\Omar\AppData\Local\Temp\Rtmpeah9J5\downloaded_packages >> Attaching package: 'hgu95av2cdf' >> The following object(s) are masked from 'package:mouse4302cdf': >> i2xy, xy2i >> AffyBatch object >> size of arrays=640x640 features (27212 kb) >> cdf=HG_U95Av2 (12625 affyids) >> number of samples=4 >> number of genes=12625 >> annotation=hgu95av2 >> notes= >> Now, following the vignette I try, >> >> > image(Dilution) >> Error in image.default(Dilution) : 'z' must be a matrix >> >> > this call should not be invoking image.default, but rather affy::image ... > your searchlist is messed up, or you > have failed to do library(affy) > > >> and then, >> >> > hist(Dilution[, 1:2]) >> Error in hist.default(Dilution[, 1:2]) : 'x' must be numeric >> >> However, the following works, >> >> plotDensity(exprs(Dilution), log="x") >> >> but the curve is not smooth at all. >> >> Other examples from the same vignette can be run with no problems. >> >> Am I missing something here? I tried the vignette examples because my own >> data was having problems with this functions. >> >> My OS is Windows 7 with R 2.13 and Bioconductor 2.8. >> >> I look forward to hear from some of you. >> >> Thanks in advance, >> >> Omar >> >> [[alternative HTML version deleted]] >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor@r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor >> > > [[alternative HTML version deleted]]