Question: cummeRbund create database ERROR
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gravatar for tjdrnjsqpf
3.3 years ago by
tjdrnjsqpf10
tjdrnjsqpf10 wrote:

hello

I'm student of Chonnam national University in south Korea.

I have problem with cummeRbund that I install in R clearly.

this is my error message

> cuff <- readCufflinks(dir="/Users/lsg/Desktop/RNA_seq/LHG/diff_out_12345", rebuild=T)
Creating database /Users/lsg/Desktop/RNA_seq/LHG/diff_out_12345/cuffData.db
Reading Run Info File /Users/lsg/Desktop/RNA_seq/LHG/diff_out_12345/run.info
Writing runInfo Table
Reading Read Group Info  /Users/lsg/Desktop/RNA_seq/LHG/diff_out_12345/read_groups.info
Writing replicates Table
Reading Var Model Info  /Users/lsg/Desktop/RNA_seq/LHG/diff_out_12345/var_model.info
Writing varModel Table
Reading /Users/lsg/Desktop/RNA_seq/LHG/diff_out_12345/genes.fpkm_tracking
Checking samples table...
Populating samples table...
Writing genes table
Reshaping geneData table
Recasting
Writing geneData table
Reading /Users/lsg/Desktop/RNA_seq/LHG/diff_out_12345/gene_exp.diff
Error in (function (classes, fdef, mtable)  : 
  unable to find an inherited method for function 'make.db.names' for signature '"SQLiteConnection", "integer"'

> cuff
CuffSet instance with:
     5 samples
     27451 genes
     0 isoforms
     0 TSS
     0 CDS
     0 promoters
     0 splicing
     0 relCDS

I don't know what is the problem.

rna-seq cummerbund • 1.2k views
ADD COMMENTlink modified 9 months ago by RamRS21k • written 3.3 years ago by tjdrnjsqpf10

Have you figured out what is the issue with this cummeRbund? Even I am getting 0 for cuff object.

ADD REPLYlink written 6 months ago by bioinforesearchquestions230
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