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. 2. When I was running the example provided in: http://bioconductor.org/packages/devel/bioc/vignettes/cummeRbund/inst/ 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) There are some other similar errors. Thanks, -Jack [[alternative HTML version deleted]]

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/ins t/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