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Old 03-11-2012, 10:45 PM   #3
Junior Member
Location: Phoenix

Join Date: May 2010
Posts: 7

Hi loyal Goff,
I have been trying running CummeRbund. As suggested I installed the latest version of cummeRbund (v1.1.3) within R 2.15.0 . The Error << Error in data.frame(index = c(1:length(samples)), sample_name = samples) arguments imply differing number of rows: 2, 0
Calls: readCufflinks -> loadGenes -> populateSampleTable -> data.frame
disappeared , but a new one showed up as copied below:
NOTE: my working directory is the ouput directory of cuffdiff. I have to mention that CDS, promoter and TSS files are empty in my case. Only Isoforms and Genes files contain results.

Loading required package: RSQLite
Loading required package: methods
Loading required package: DBI
Loading required package: ggplot2
Loading required package: reshape2
Creating database /cuffdiff_outputs/cuffData.db
Reading /cuffdiff_outputs/genes.fpkm_tracking
Checking samples table...
Populating samples table...
Writing genes table
Reshaping geneData table
Error in, ... ~ measurement)) :
could not find function "cast"
Calls: readCufflinks -> loadGenes ->

Thanks for your help.
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