Hi, I have downloaded/installed cummeRbund vis biocLite and have run it on 2 sets of samples. I have 2 sets of cuffdiff 1.3.0 results and they both load fine into cummeRbund as follows. library(cummeRbund) setwd("C:/Users/mark/Documents/Cross/cufflinks_data/diff_blad_1_3_0/di ff_blad_1_3_0") cuff<-readCufflinks() dens<-csDensity(genes(cuff)) dens # This works fine and displays a density plot. But, if I run all this again on a different set of samples, I get this. library(cummeRbund) setwd("C:/Users/mark/Documents/Cross/cufflinks_data/diff_colon_1_3_0/d iff_colon_1_3_0") cuff<-readCufflinks() dens<-csDensity(genes(cuff)) dens Error: attempt to apply non-function Any ideas how I can fix this; looks like there is a difference in results somewhere but all files present in both sets of data. Thank you.

Hi, On Wed, Jan 11, 2012 at 9:28 AM, john herbert <arraystruggles at="" gmail.com=""> wrote: > Hi, > I have downloaded/installed cummeRbund vis biocLite and have run it on > 2 sets of samples. > > I have 2 sets of cuffdiff 1.3.0 results and they both load fine into > cummeRbund as follows. > > library(cummeRbund) > > setwd("C:/Users/mark/Documents/Cross/cufflinks_data/diff_blad_1_3_0/ diff_blad_1_3_0") > > cuff<-readCufflinks() > > dens<-csDensity(genes(cuff)) > dens > > # This works fine and displays a density plot. But, if I run all this > again on a different set of samples, I get this. > > library(cummeRbund) > setwd("C:/Users/mark/Documents/Cross/cufflinks_data/diff_colon_1_3_0 /diff_colon_1_3_0") > cuff<-readCufflinks() > dens<-csDensity(genes(cuff)) > dens > > Error: attempt to apply non-function > > Any ideas how I can fix this; looks like there is a difference in > results somewhere but all files present in both sets of data. I "like" to peruse the source code of the packages I'm using to see what's cooking under the hood (you can download the source package from the package site at bioconductor.org). To get a better idea of where to start digging in the source, call "traceback()" in your R workspace after the error occurs. R will print a stack trace that shows you the series of function calls that landed you in the fix you're in now. The stack trace will act as a trail of breadcrumbs you can use to follow the execution path of your code in hopes of finding which expectations aren't met in your program that causes the error. HTH, -steve -- Steve Lianoglou Graduate Student: Computational Systems Biology ?| Memorial Sloan-Kettering Cancer Center ?| Weill Medical College of Cornell University Contact Info: http://cbio.mskcc.org/~lianos/contact

Hi Loyal, Valerie. Thank you all for taking a look. Valerie's suggestion;?> head( fpkmMatrix(genes(cuff)))? ? ? ? ? ? TumColon NormColonXLOC_000001 ? ? <na> ? ? ?<na>XLOC_000002 ? ? <na> <na>XLOC_000003 ? ? <na> ? ? ?<na>XLOC_000004 ? ? <na> <na>XLOC_000005 ? ? <na> ? ? ?<na>XLOC_000006 ? ? <na> ? ? ?<na> Makes it look like there is some data not getting loaded. So I re-transferred data and unzipped the data files and this time all was all fine. Sorry about that; It now works fine. Thank you. John. On Wed, Jan 11, 2012 at 10:01 PM, Loyal Goff <lgoff at="" csail.mit.edu=""> wrote: > Hi John, > If you provide the cuffData.db file for the one colon sample, I will take a look to see what's happening. > > > Cheers, > Loyal > > > On Jan 11, 2012, at 3:15 PM, Valerie Obenchain wrote: > >> cc'ing Loyal (package maintainer) >> >> >> John, >> >> Is is possible for you to provide the colon file so we can reproduce the error? >> >> It looks like the colon data can be read in successfully but is failing when you try to produce the density plot. Is that correct? >> >> this works >> >> ? ?cuff<-readCufflinks() >> >> but this doesn't >> >> ? ?dens<-csDensity(genes(cuff)) >> >> If this is the case you can further investigate the cuff object by inspecting the 'genes' object >> >> ? ?samples(genes(cuff)) >> ? ?features(genes(cuff)) >> >> The data that are plotted in cdDensity() are >> >> ? ?fpkmMatrix(genes(cuff)) >> >> >> Valerie >> >> >> >> >> >> On 01/11/2012 07:33 AM, john herbert wrote: >>> Thank you Steve, that is helpful. Based on what I get from traceback >>> and the message being "Error: attempt to apply non-function", would I >>> be right in thinking the lapply and seq_along being the problem? >>> >>> I also notice a big difference in size between the cuffData database >>> files that cummeRbund makes. >>> Colon that does not work = ~3Mb >>> Blad that does work = ~115Mb >>> >>> All other cuffdiff result files are of a similar size between Colon >>> and Blad samples. >>> >>> John. >>> >>> >>> >>>> densError: attempt to apply non-function> ?traceback()9: FUN(1L[[1L]], ...)8: lapply(seq_along(data), function(i) { ? ? ? layer<- layers[[i]] ? ? ? layerd<- data[[i]] ? ? ? grobs<- matrix(list(), nrow = nrow(layerd), ncol = ncol(layerd)) ? ? ? for (i in seq_len(nrow(layerd))) { ? ? ? ? ? for (j in seq_len(ncol(layerd))) { ? ? ? ? ? ? ? scales<- list(x = .$scales$x[[j]]$clone(), y = .$scales$y[[i]]$clone()) ? ? ? ? ? ? ? details<- coord$compute_ranges(scales) ? ? ? ? ? ? ? grobs[[i, j]]<- layer$make_grob(layerd[[i, j]], ? ? ? ? ? ? ? ? ? ?details, coord) ? ? ? ? ? } ? ? ? } ? ? ? grobs ? })7: get(x, envir = this, inherits = inh)(this, ...)6: facet$make_grobs(data, layers, cs)5: ggplot_build(plot)4: ggplotGrob(x, ...)3: grid.draw(ggplotGrob(x, ...))2: print.ggplot(list(data = list(gene_id = character(0), sample_name = integer(0), ? ? ? ?fpkm = numeric(0), conf_hi = numeric(0), conf_lo = numeric(0), ? ? ? ?quant_status = character(0)), layers = list(<environment>), ? ? ? ?scales =<environment>, mapping = list(), options = list( ? ? ? ? ? title = "genes", labels = list(x = "log10(fpkm)", group = "sample_name", ? ? ? ? ? ? ? ?colour = "sample_name", fill = "sample_name", y = "density")), ? ? ? ?coordinates =<environment>, facet =<environment>, plot_env =<environment>))1: print(list(data = list(gene_id = character(0), sample_name = integer(0), ? ? ? ?fpkm = numeric(0), conf_hi = numeric(0), conf_lo = numeric(0), ? ? ? ?quant_status = character(0)), layers = list(<environment>), ? ? ? ?scales =<environment>, mapping = list(), options = list( ? ? ? ? ? title = "genes", labels = list(x = "log10(fpkm)", group = "sample_name", ? ? ? ? ? ? ? ?colour = "sample_name", fill = "sample_name", y = "density")), ? ? ? ?coordinates =<environment>, facet =<environment>, plot_env =<environment>)) >>> On Wed, Jan 11, 2012 at 2:56 PM, Steve Lianoglou >>> <mailinglist.honeypot at="" gmail.com=""> ?wrote: >>>> Hi, >>>> >>>> On Wed, Jan 11, 2012 at 9:28 AM, john herbert<arraystruggles at="" gmail.com=""> ?wrote: >>>>> Hi, >>>>> I have downloaded/installed cummeRbund vis biocLite and have run it on >>>>> 2 sets of samples. >>>>> >>>>> I have 2 sets of cuffdiff 1.3.0 results and they both load fine into >>>>> cummeRbund as follows. >>>>> >>>>> library(cummeRbund) >>>>> >>>>> setwd("C:/Users/mark/Documents/Cross/cufflinks_data/diff_blad_1_ 3_0/diff_blad_1_3_0") >>>>> >>>>> cuff<-readCufflinks() >>>>> >>>>> dens<-csDensity(genes(cuff)) >>>>> dens >>>>> >>>>> # This works fine and displays a density plot. But, if I run all this >>>>> again on a different set of samples, I get this. >>>>> >>>>> library(cummeRbund) >>>>> setwd("C:/Users/mark/Documents/Cross/cufflinks_data/diff_colon_1 _3_0/diff_colon_1_3_0") >>>>> cuff<-readCufflinks() >>>>> dens<-csDensity(genes(cuff)) >>>>> dens >>>>> >>>>> Error: attempt to apply non-function >>>>> >>>>> Any ideas how I can fix this; looks like there is a difference in >>>>> results somewhere but all files present in both sets of data. >>>> I "like" to peruse the source code of the packages I'm using to see >>>> what's cooking under the hood (you can download the source package >>>> from the package site at bioconductor.org). >>>> >>>> To get a better idea of where to start digging in the source, call >>>> "traceback()" in your R workspace after the error occurs. R will print >>>> a stack trace that shows you the series of function calls that landed >>>> you in the fix you're in now. The stack trace will act as a trail of >>>> breadcrumbs you can use to follow the execution path of your code in >>>> hopes of finding which expectations aren't met in your program that >>>> causes the error. >>>> >>>> HTH, >>>> -steve >>>> >>>> -- >>>> Steve Lianoglou >>>> Graduate Student: Computational Systems Biology >>>> ?| Memorial Sloan-Kettering Cancer Center >>>> ?| Weill Medical College of Cornell University >>>> Contact Info: http://cbio.mskcc.org/~lianos/contact >>> _______________________________________________ >>> 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 >> >> >