Cummerbund Returns 0 Sample

Question

[madkitty]

When running readcufflinks on the default folder containing our 3 samples it returns "0 sample". I tried readcufflinks on the sample folders provided by the package and it works well. I set up R default folder under the root as R_data so technically it should find the samples automatically.. What would be a good solution so readCufflinks can find our 3 samples?

   # Test with our set of 3 samples
  library(cummeRbund)     
  cuff<-readCufflinks ()
  cuff

  CuffSet instance with:
           0 samples
           0 genes
           0 isoforms
           0 TSS
           0 CDS
           0 promoters
           0 splicing
          0 relCDS

  # Test with the sample files provided with the cummeRbund package, works fine
  cuff<-readCufflinks(system.file("extdata", package="cummeRbund"))
  cuff 
  CuffSet instance with:
           3 samples
           400 genes
           1203 isoforms
           662 TSS
           906 CDS
           1062 promoters
          1986 splicing
           990 relCDS

Answer 1

[lkw222]

Did either of you find a solution to this problem? I am having the same issue as in the original post.

Answer 2

[vincr]

I have solved this by:

• using R version 3.1.3 or anterior
• adding the rebuild=T argument to readCufflinks (data<-readCufflinks(..., rebuild = T))

Hope that helps...

[eculfa]

hi,

I have the same problem. I tried your rebuild command and it didn't work. But I am terrible at coding anyway so I thought I missed something. I have attempted to feed the command by modifying it and this was what i got. What do you suggest I do? Thanks, Efraim

readCufflinks (data<-readCufflinks(..., rebuild = T)) Error in file.path(dir, dbFile) : '...' used in an incorrect context readCufflinks (data<-readCufflinks(Cuffdiff, rebuild = T)) Error in file.path(dir, dbFile) : object 'Cuffdiff' not found readCufflinks (data<-readCufflinks(Cuffdata, rebuild = T)) Error in file.path(dir, dbFile) : object 'Cuffdata' not found readCufflinks ((data<-readCufflinks(rebuild = T))

Answer 3

[super]

I have similar questions but no one knew the answers.

CuffSet instance with: 2 samples 25264 genes 0 isoforms 0 TSS 0 CDS 0 promoters 0 splicing 0 relCDS

but I have 6 samples (3 samples in 1 group), I don't know why it happened.