This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Error in cummeRbund R library package (Error: Columns index not found)

Hi,

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/run.info

Writing runInfo Table

Reading Read Group Info  /Users/admin/Desktop/RNA_seq_Analysis/cuffdiff/read_groups.info

Writing replicates Table

Reading Var Model Info  /Users/admin/Desktop/RNA_seq_Analysis/cuffdiff/var_model.info

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) >

cuff_data

CuffSet instance with:

0 samples

0 genes

0 isoforms

0 TSS

0 CDS

0 promoters

0 splicing

0 relCDS

rnaseq cummerbund cuffdiff
• 2,478 views • link
updated by Abdul Rawoof Abdul Rawoof • written by bioinforesearchquestions bioinforesearchquestions

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

• 1 views • link
written by Nitin Narwade Nitin Narwade

Can you please post the output of this command:

packageVersion("cummeRbund")
• 1 views • link
written by Nitin Narwade Nitin Narwade

1 answer

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

• 0 views • link
written by Abdul Rawoof Abdul Rawoof

Log in to answer this question.

More posts like this