Hi! I'm using the Cufflinks protocol published in Nature (Vol.7 No.3, 2012) and facing a problem with cummeRbund while processing my results. Something about the SQL-Statement seems to be wrong. Here are the commands, I used:
Already tried version 1.0.0 and 1.1.5 without any success.
Although the error is generated, the database file: cuffData.db has been created. While using the read-command again I get a CuffSet-Instance, but it seems to be incomplete:
I have used cuffdiff on 6 samples in 2 conditions. Could there occur any problems with the sample/condition-description, the one has a '+' and the other a '-' ?!?
Many thanks in advance!
Lukas
Code:
> library(cummeRbund) > cuff<-readCufflinks() Creating database /media/md0/rnaseq/cuffData.db Reading /media/md0/rnaseq/genes.fpkm_tracking Checking samples table... Populating samples table... Writing genes table Reshaping geneData table Recasting Writing geneData table Error in sqliteExecStatement(con, statement, bind.data) : RS-DBI driver: (unable to bind data for parameter ':status')
Although the error is generated, the database file: cuffData.db has been created. While using the read-command again I get a CuffSet-Instance, but it seems to be incomplete:
Code:
CuffSet instance with: 1 samples 116962 genes 0 isoforms 0 TSS 0 CDS 0 promoters 0 splicing 0 relCDS
Many thanks in advance!
Lukas
Comment