[BioC] CummeRbund Error

[john herbert]

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
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>>
>>
>