On 07/02/2012 12:33 PM, Jack Luo wrote: > Sure, see below: > >> sessionInfo() > R version 2.15.1 (2012-06-22) > Platform: i386-pc-mingw32/i386 (32-bit) > > locale: > [1] LC_COLLATE=English_United States.1252 > [2] LC_CTYPE=English_United States.1252 > [3] LC_MONETARY=English_United States.1252 > [4] LC_NUMERIC=C > [5] LC_TIME=English_United States.1252 > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] cummeRbund_1.2.0 reshape2_1.2.1 ggplot2_0.9.1 ^^^^^ Here you go. H. > [4] RSQLite_0.11.1 DBI_0.2-5 BiocInstaller_1.4.7 > > loaded via a namespace (and not attached): > [1] colorspace_1.1-1 dichromat_1.2-4 digest_0.5.2 grid_2.15.1 > > [5] labeling_0.1 MASS_7.3-19 memoise_0.1 munsell_0.3 > > [9] plyr_1.7.1 proto_0.3-9.2 RColorBrewer_1.0-5 scales_0.2.1 > > [13] stringr_0.6 tools_2.15.1 > > Thanks, > > -Jack > > On Mon, Jul 2, 2012 at 3:06 PM, Dan Tenenbaum <dtenenba at="" fhcrc.org=""> wrote: > >> Hi Jack, >> >> On Mon, Jul 2, 2012 at 12:01 PM, Jack Luo <jluo.rhelp at="" gmail.com=""> wrote: >>> Hi Val, >>> >>> Thanks. See below: >>> >>>> library(cummeRbund) >>>> cuff <- readCufflinks(dir=system.file("extdata", package="cummeRbund")) >>>> disp<-dispersionPlot(genes(cuff)) >>> Error: could not find function "dispersionPlot" >>>> dens<-csDensity(genes(cuff)) >>>> densRep<-csDensity(genes(cuff),replicates=T) >>>> b<-csBoxplot(genes(cuff)) >>>> b >>>> brep<-csBoxplot(genes(cuff),replicates=T) >>>> brep >>>> s<-csScatter(genes(cuff),"hESC","Fibroblasts",smooth=T) >>>> s >>>> dend<-csDendro(genes(cuff)) >>>> dend.rep<-csDendro(genes(cuff),replicates=T) >>> Error in csDendro(genes(cuff), replicates = T) : >>> unused argument(s) (replicates = T) >>>> >>>> m<-MAplot(genes(cuff),"hESC","Fibroblasts") >>>> m >>> Warning message: >>> Removed 57 rows containing missing values (geom_point). >>>> mCount<-MAplot(genes(cuff),"hESC","Fibroblasts",useCount=T) >>> Error in .local(object, x, y, logMode, pseudocount, ...) : >>> unused argument(s) (useCount = TRUE) >>>> mCount >>> Error: object 'mCount' not found >>> >> >> That is helpful but we still need the output of >> >> sessionInfo() >> >> because that tells us what platform you're on, what version of R you >> are running, and what version of various packages you have loaded. >> Run the sessionInfo command after loading cummeRbund. >> >> Thanks, >> Dan >> >> >>> >>> Let me know if that's what you need, thanks. >>> >>> -Jack >>> >>> On Sun, Jul 1, 2012 at 5:52 PM, Valerie Obenchain <vobencha at="" fhcrc.org=""> >>> wrote: >>>> >>>> Jack, >>>> >>>> In order for us to help we need some more information. >>>> >>>> Please provide a small reproducible example of the code you are >> executing >>>> and the error. Below you've provided the errors but no preceding code. >> Also >>>> send the output of typing sessionInfo() at the command prompt. >>>> >>>> fyi, I've cc'd the package maintainer. >>>> >>>> Valerie >>>> >>>> >>>> >>>> >>>> On 07/01/12 05:50, Jack Luo wrote: >>>>> >>>>> Hi Dan, >>>>> >>>>> Thanks for your email. Yeah, I installed the package using >>>>> biocLite("cummeRbund"). There are some functions that work well, but >> not >>>>> those functions I listed for error msg, not sure why. >>>>> >>>>> Thanks, >>>>> >>>>> -Jack >>>>> >>>>> On Fri, Jun 29, 2012 at 4:56 PM, Dan Tenenbaum<dtenenba at="" fhcrc.org=""> >>>>> wrote: >>>>> >>>>>> Hi Jack, >>>>>> >>>>>> On Fri, Jun 29, 2012 at 1:41 PM, Jack Luo<jluo.rhelp at="" gmail.com=""> >> wrote: >>>>>>> >>>>>>> Hi, >>>>>>> >>>>>>> I am a newbie to RNA-seq data and try to learn using the cummeRbund >>>>>>> package. Some simple questions are: >>>>>>> >>>>>>> 1. My OS is windows 7. I have no problem installing the cummeRbund in >>>>>>> R, >>>>>>> but do I need to install cufflinks? I thought there is only linux and >>>>>>> mac >>>>>>> version of cufflinks, not windows. >>>>>> >>>>>> Although the vignette says you need cufflinks, you don't, really. You >>>>>> just need some files produced by cufflinks. >>>>>> >>>>>>> 2. When I was running the example provided in: >>>>>>> >>>>>> >>>>>> >> http://bioconductor.org/packages/devel/bioc/vignettes/cummeRbund/in st/doc/cummeRbund-manual.pdf >>>>>>> >>>>>>> I run into several errors: >>>>>>> A. Error: could not find function "dispersionPlot" >>>>>>> B. dend.rep<-csDendro(genes(cuff),replicates=T) >>>>>>> Error in csDendro(genes(cuff), replicates = T) : >>>>>>> unused argument(s) (replicates = T) >>>>>>> C. mCount<-MAplot(genes(cuff),"hESC","Fibroblasts",useCount=T) >>>>>>> Error in .local(object, x, y, logMode, pseudocount, ...) : >>>>>>> unused argument(s) (useCount = TRUE) >>>>>>> >>>>>> How did you install cummeRbund? >>>>>> Try installing it as follows: >>>>>> biocLite("cummeRbund") >>>>>> >>>>>> Also, when reporting errors, please report the command(s) that caused >>>>>> the errors and include the output of sessionInfo(). >>>>>> >>>>>> Thanks, >>>>>> Dan >>>>>> >>>>>> >>>>>>> There are some other similar errors. >>>>>>> >>>>>>> Thanks, >>>>>>> >>>>>>> -Jack >>>>>>> >>>>>>> [[alternative HTML version deleted]] >>>>>>> >>>>>>> _______________________________________________ >>>>>>> Bioconductor mailing list >>>>>>> Bioconductor at 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]] >>>>> >>>>> _______________________________________________ >>>>> Bioconductor mailing list >>>>> Bioconductor at 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]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > -- Hervé Pagès Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M1-B514 P.O. 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