Question: Error in cummeRbund R library package (Error: Columns index not found)
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gravatar for bioinforesearchquestions
7 months ago by
United States
bioinforesearchquestions210 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 • 334 views
ADD COMMENTlink modified 7 months ago by genomax67k • written 7 months ago by bioinforesearchquestions210

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

ADD REPLYlink modified 7 months ago • written 7 months ago by Nitin Narwade380

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

ADD REPLYlink written 7 months ago by bioinforesearchquestions210

Can you please post the output of this command:

packageVersion("cummeRbund")
ADD REPLYlink modified 7 months ago • written 7 months ago by Nitin Narwade380

packageVersion("cummeRbund") [1] ‘2.16.0

ADD REPLYlink written 6 months ago by bioinforesearchquestions210
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