[BioC] CummeRbund Error

[john herbert]

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