Question: Error in cummeRbund R library package (Error: Columns index not found)
0
gravatar for bioinforesearchquestions
16 months ago by
United States
bioinforesearchquestions270 wrote:

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

cuffdiff cummerbund rnaseq • 622 views
ADD COMMENTlink modified 7 months ago by Abdul Rawoof60 • written 16 months ago by bioinforesearchquestions270

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

ADD REPLYlink modified 16 months ago • written 16 months ago by Nitin Narwade440

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

ADD REPLYlink written 16 months ago by bioinforesearchquestions270

Can you please post the output of this command:

packageVersion("cummeRbund")
ADD REPLYlink modified 16 months ago • written 16 months ago by Nitin Narwade440

packageVersion("cummeRbund") [1] ‘2.16.0

ADD REPLYlink written 14 months ago by bioinforesearchquestions270
0
gravatar for Abdul Rawoof
7 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 7 months ago by Abdul Rawoof60
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