Entering edit mode
8.9 years ago
tjdrnjsqpf
▴
10
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.
Have you figured out what is the issue with this cummeRbund? Even I am getting 0 for cuff object.