Hi list,
Is the cummeRbund wrapper on Galaxy yet functional? I've got some replicates that I'm trying to test for a user on our local Galaxy, but I just can't get the program to behave.
Using cuffdiff v2.2.0 604fa75232a2
cummeRbund version 0.0.7, 137aab1d9ac1
R 2.15.2 and 3.0.1 (tried both)
Last galaxy-dist/stable changeset: 7a7985a007fb
I ran cuffdiff like so:
Transcripts 83: Cuffmerge on data 6, data 67, and others: merged transcripts
Name control
Add replicate 44: Tophat2 on data 1 and data 6: accepted_hits (ran as single-end fastq)
Add replicate 54: Tophat2 on data 2 and data 6: accepted_hits (ran as single-end fastq)
Name sample
Add replicate 59: Tophat2 on data 3 and data 6: accepted_hits (ran as single-end fastq)
Add replicate 64: Tophat2 on data 4 and data 6: accepted_hits (ran as single-end fastq)
Library normalization method geometric
Dispersion estimation method pooled
False Discovery Rate 0.05
Min Alignment Count 10
Use multi-read correct No
Perform Bias Correction No
Include Read Group Datasets No
Set Additional Parameters? (not recommended for paired-end reads) No
Here's what I get when I run cummeRbund:
(From Galaxy, with R 2.15.2)
Creating database //path/job_working_directory/005/5051/galaxy_dataset_16602.dat
Reading //path/dataset_files/009/dataset_9861.dat
Checking samples table...
Populating samples table...
Writing genes table
Reshaping geneData table
Recasting
Writing geneData table
Reading //path/dataset_files/009/dataset_9861.dat
Error in function (classes, fdef, mtable) :
unable to find an inherited method for function 'make.db.names' for signature '"SQLiteConnection", "NULL"'
Calls: readCufflinks ... make.db.names -> .valueClassTest -> is -> <Anonymous>
Execution halted
(From R interpreter on command line, R = 3.0.1)
Reading //path/dataset_files/009/dataset_9842.dat
Checking samples table...
Populating samples table...
Writing genes table
Reshaping geneData table
Recasting
Writing geneData table
Reading //path/dataset_files/009/dataset_9842.dat
Error in (function (classes, fdef, mtable) :
unable to find an inherited method for function 'make.db.names' for signature '"SQLiteConnection", "NULL"'
In addition: Warning message:
attributes are not identical across measure variables; they will be dropped
I tried changing the group names in cuffdiff but no luck. No spaces or funny characters.
Thanks for any insight,
Carrie Ganote