Question: Error in cummeRbund R library package (Error: Columns index not found)
gravatar for bioinforesearchquestions
20 months ago by
United States
bioinforesearchquestions280 wrote:


With the below cuffdiff output, I already generated plots using cummeRbund package. But now, I am getting some error. What could be the reason? Have anyone faced it before?

cuff_data <- readCufflinks("/Users/admin/Desktop/RNA_seq_Analysis/cuffdiff", rebuild = T)

Creating database /Users/admin/Desktop/RNA_seq_Analysis/cuffdiff/cuffData.db

Reading Run Info File /Users/admin/Desktop/RNA_seq_Analysis/cuffdiff/

Writing runInfo Table

Reading Read Group Info  /Users/admin/Desktop/RNA_seq_Analysis/cuffdiff/

Writing replicates Table

Reading Var Model Info  /Users/admin/Desktop/RNA_seq_Analysis/cuffdiff/

Writing varModel Table

Reading /Users/admin/Desktop/RNA_seq_Analysis/cuffdiff/genes.fpkm_tracking

Checking samples table...

Populating samples table...

Error: Columns `index` not found

In addition: There were 50 or more warnings (use warnings() to see the first 50) >


CuffSet instance with:

0 samples

0 genes

0 isoforms



0 promoters

0 splicing

0 relCDS

cuffdiff cummerbund rnaseq • 731 views
ADD COMMENTlink modified 11 months ago by Abdul Rawoof60 • written 20 months ago by bioinforesearchquestions280

Why you are using rebuild = T option? Have you tried without using that option?

ADD REPLYlink modified 20 months ago • written 20 months ago by Nitin Narwade440

Yeah, tried without that as well. Same error and empty cuffset instance.

ADD REPLYlink written 19 months ago by bioinforesearchquestions280

Can you please post the output of this command:

ADD REPLYlink modified 19 months ago • written 19 months ago by Nitin Narwade440

packageVersion("cummeRbund") [1] ‘2.16.0

ADD REPLYlink written 18 months ago by bioinforesearchquestions280
gravatar for Abdul Rawoof
11 months ago by
Abdul Rawoof60
United States
Abdul Rawoof60 wrote:

Update cummeRbund package to version 2.26.0 Hope, this will resolve your error issue.

ADD COMMENTlink written 11 months ago by Abdul Rawoof60
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