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Question: question regarding using cummeRbund package
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gravatar for Jack Luo
5.4 years ago by
Jack Luo340
Jack Luo340 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@fhcrc.org> wrote: > Hi Jack, > > On Fri, Jun 29, 2012 at 1:41 PM, Jack Luo <jluo.rhelp@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@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]]
ADD COMMENTlink modified 5.4 years ago by Valerie Obenchain ♦♦ 6.4k • written 5.4 years ago by Jack Luo340
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gravatar for Valerie Obenchain
5.4 years ago by
Valerie Obenchain ♦♦ 6.4k
United States
Valerie Obenchain ♦♦ 6.4k 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
ADD COMMENTlink written 5.4 years ago by Valerie Obenchain ♦♦ 6.4k
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 Let me know if that's what you need, thanks. -Jack On Sun, Jul 1, 2012 at 5:52 PM, Valerie Obenchain <vobencha@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@fhcrc.org> >> wrote: >> >> Hi Jack, >>> >>> On Fri, Jun 29, 2012 at 1:41 PM, Jack Luo<jluo.rhelp@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/inst/doc/**cummeRbund-manual.pdf<http: bioconductor.or="" g="" 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) >>>> >>>> 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@r-project.org >>>> https://stat.ethz.ch/mailman/**listinfo/bioconductor<https: stat="" .ethz.ch="" mailman="" listinfo="" bioconductor=""> >>>> Search the archives: >>>> >>> http://news.gmane.org/gmane.**science.biology.informatics.**conduc tor<http: news.gmane.org="" gmane.science.biology.informatics.conductor=""> >>> >>> [[alternative HTML version deleted]] >> >> ______________________________**_________________ >> Bioconductor mailing list >> Bioconductor@r-project.org >> https://stat.ethz.ch/mailman/**listinfo/bioconductor<https: stat.e="" thz.ch="" mailman="" listinfo="" bioconductor=""> >> Search the archives: http://news.gmane.org/gmane.** >> science.biology.informatics.**conductor<http: news.gmane.org="" gmane="" .science.biology.informatics.conductor=""> >> > > [[alternative HTML version deleted]]
ADD REPLYlink written 5.4 years ago by Jack Luo340
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/ 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) >>>>> >>>> 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 >> >> >
ADD REPLYlink written 5.4 years ago by Dan Tenenbaum ♦♦ 8.2k
Hi Jack, On 07/02/2012 12:06 PM, Dan Tenenbaum 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" It looks like the dispersionPlot() function is new in cummeRbund version 1.99.* (BioC devel), so your problem is very likely that you're trying to run code that belongs to the vignette of cummeRbund 1.99.* while you have some older version of the package installed. Hard to know for sure without you providing the output of your sessionInfo(). In any case, make sure you look at the right vignette/examples i.e. that they belong to the package you are actually using. For example using browseVignettes() is a much safer way than picking the vignette from somewhere on the web e.g. from http://bioconductor.org/packages/2.11/bioc/html/cummeRbund.html This is because browseVignettes() shows you the list of vignettes that belong to the packages you installed so they are guaranteed to match. Cheers, H. >>> 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 /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) >>>>>> >>>>> 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 >>> >>> >> > > _______________________________________________ > 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. Box 19024 Seattle, WA 98109-1024 E-mail: hpages at fhcrc.org Phone: (206) 667-5791 Fax: (206) 667-1319
ADD REPLYlink written 5.4 years ago by Hervé Pagès ♦♦ 13k
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 [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@fhcrc.org> wrote: > Hi Jack, > > On Mon, Jul 2, 2012 at 12:01 PM, Jack Luo <jluo.rhelp@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@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@fhcrc.org> > >>> wrote: > >>> > >>>> Hi Jack, > >>>> > >>>> On Fri, Jun 29, 2012 at 1:41 PM, Jack Luo<jluo.rhelp@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@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@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]]
ADD REPLYlink written 5.4 years ago by Jack Luo340
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. Box 19024 Seattle, WA 98109-1024 E-mail: hpages at fhcrc.org Phone: (206) 667-5791 Fax: (206) 667-1319
ADD REPLYlink written 5.4 years ago by Hervé Pagès ♦♦ 13k
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