[BioC] CummeRbund Error

[Steve Lianoglou]

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