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Old 08-02-2012, 05:29 AM   #1
NRiddiford
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Location: Ireland

Join Date: Jul 2012
Posts: 6
Default CummeRbund error

Hi,

I'm running cummeRbund and can't get around this error:

library(cummeRbund)
setwd ("<path>")
cuff_data <- readCufflinks('diff_out')
csDensity(genes(cuff_data))
Error in sqliteExecStatement(con, statement, bind.data) :
RS-DBI driver: (error in statement: database is locked)

Does anyone know a solution to this problem?

R v. 2.15.0
Cufflinks v. 1.3.0
CummeRbund v. 2.15.0

Thanks,

Nick
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Old 08-08-2012, 04:41 PM   #2
lgoff
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Location: Cambridge, MA

Join Date: Feb 2008
Posts: 82
Default

Quote:
Originally Posted by NRiddiford View Post
Hi,

I'm running cummeRbund and can't get around this error:

library(cummeRbund)
setwd ("<path>")
cuff_data <- readCufflinks('diff_out')
csDensity(genes(cuff_data))
Error in sqliteExecStatement(con, statement, bind.data) :
RS-DBI driver: (error in statement: database is locked)

Does anyone know a solution to this problem?

R v. 2.15.0
Cufflinks v. 1.3.0
CummeRbund v. 2.15.0

Thanks,

Nick
Hi Nick,
I have seen this error only once before and the issue in this case was that the database was on an NFS mount that was interfering with the normal operation of the SQLite database. Is your working directory also on an NFS mount? If so, is it possible to try and move the directory to a different mount and see if this resolves the error?

-Loyal
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Old 08-23-2012, 02:53 AM   #3
NRiddiford
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Location: Ireland

Join Date: Jul 2012
Posts: 6
Default

Thanks lgoff,

I've been away from the computer for the past few weeks, but will give this a go and let you know.

Best,

Nick
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Old 09-14-2012, 04:05 AM   #4
IBseq
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Location: uk

Join Date: Jul 2012
Posts: 56
Default

HI, anyone has ever had this error?No idea what to do...any suggestion??All my samples have worked except this one...

> library(cummeRbund)
Loading required package: RSQLite
Loading required package: DBI
Loading required package: ggplot2
Loading required package: reshape2
> cuff<-readCufflinks("~/Cuffdiff/hpv18")
Creating database ~/Cuffdiff/hpv18/cuffData.db
Reading ~/Cuffdiff/hpv18/genes.fpkm_tracking
Checking samples table...
Populating samples table...
Writing genes table
Reshaping geneData table
Recasting
Writing geneData table
Reading ~/Cuffdiff/hpv18/gene_exp.diff
Error in function (classes, fdef, mtable) :
unable to find an inherited method for function "make.db.names", for signature "SQLiteConnection", "integer"

thanks,
ib
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Old 03-20-2013, 06:11 PM   #5
Charitra
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Location: Seoul, Korea

Join Date: Feb 2013
Posts: 57
Default CummeRbund error

Hi
I have recently installed R and cummeRbund but I dont know how to use it.

I have completed my tophat followed by cufflinks run on server. and I am using desktop for R within :
> getwd()
"C:/Documents and Settings/Charitra/My Documents"

> cuff_data <- readCufflinks('diff_out')
> csDensity(genes(cuff_data))
Error in sqliteExecStatement(con, statement, bind.data) :
RS-DBI driver: (error in statement: near ")": syntax error)

can someone tell me which files are to be kept in my working directory from Cufflinks results....??? to produce followings:

1. Plot the distribution of expression levels:
> csDensity(genes(cuff_data))
2. Compare the expression of each gene in two conditions with a scatter plot
> csScatter(genes(cuff_data), 'C1', 'C2')
3. Create a volcano plot to inspect differentially expressed genes:
> csVolcano(genes(cuff_data), 'C1', 'C2')
4. Plot expression levels for genes of interest with bar plots (Fig. 9a):
> mygene < - getGene(cuff_data,'regucalcin')
> expressionBarplot(mygene)
5. Plot individual isoform expression levels of selected genes of interest with bar plots
> expressionBarplot(isoforms(mygene))

I followed Coe Trapnell, Nature Protocol for Vol.7 No.3 | 2012
Please help me oout if you can ?
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Old 07-26-2013, 11:18 AM   #6
wacguy
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Location: NC

Join Date: Sep 2012
Posts: 24
Default did you solve it?

Hi Charitra,

Did you mennage to solve the problem; I am having the same.

Thanks a lot,
Guy
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