Hello,

I’m getting an error message when trying to run csHeatmap from CummerBund.  All other functions are working fine so I’m thinking that a required package is not being loaded and the function is not available it.  Any thoughts on what that might be.  I’m not seeing any documentation out there that has this specific problem.  The error seems to be common but I can’t find the package that might not be there.  All other required packages (from the documentation) have been installed.

Thanks,

todd

R code:

library(cummeRbund)

cuff <- readCufflinks(dir=cuff.dir)

features <- cuff@isoforms
features

h <- csHeatmap(features, cluster='both')
h


Output (Error is at the end):


Loading cummeRbund...
Loading required package: BiocGenerics
Loading required package: methods

Attaching package: ‘BiocGenerics’

The following object(s) are masked from ‘package:stats’:

    xtabs

The following object(s) are masked from ‘package:base’:

    anyDuplicated, cbind, colnames, duplicated, eval, Filter, Find,
    get, intersect, lapply, Map, mapply, mget, order, paste, pmax,
    pmax.int, pmin, pmin.int, Position, rbind, Reduce, rep.int,
    rownames, sapply, setdiff, table, tapply, union, unique

Loading required package: RSQLite
Loading required package: DBI
Loading required package: ggplot2
Loading required package: reshape2
Loading required package: fastcluster

Attaching package: ‘fastcluster’

The following object(s) are masked from ‘package:stats’:

    hclust

Loading required package: rtracklayer
Loading required package: GenomicRanges
Loading required package: IRanges
Loading required package: Gviz
Loading required package: grid

Read cuffdiff data...

Getting isoforms...
CuffData instance with:
         25177 features and 2 samples
Warning messages:
1: Removed 4202 rows containing non-finite values (stat_density).
2: Removed 4495 rows containing non-finite values (stat_density).
Warning messages:
1: Removed 4202 rows containing non-finite values (stat_density).
2: Removed 4495 rows containing non-finite values (stat_density).
Warning message:
Removed 3379 rows containing missing values (geom_point).
Error in function (classes, fdef, mtable)  :
  unable to find an inherited method for function ‘csHeatmap’ for signature ‘"CuffData"’
Calls: csHeatmap -> <Anonymous>
Execution halted



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