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Old 04-16-2012, 11:51 PM   #1
dadada4ever
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Location: Beijing

Join Date: Mar 2010
Posts: 18
Unhappy Problem with cummeRbund and RSQLite :(

Hi there, I have a problem in using cummeRbund and the issue is similar with the thread http://seqanswers.com/forums/showthread.php?t=18830 but not the same. Hope anyone can help me to solve this question..

I use the R(2.15.0) and cummeRbund 1.2.0.
Code:
> library(cummeRbund)
Loading required package: RSQLite
Loading required package: DBI
Loading required package: ggplot2
Loading required package: reshape2
> cuff<-readCufflinks("cuffdata_120417")
Creating database cuffdata_120417/cuffData.db
Reading cuffdata_120417/genes.fpkm_tracking
Checking samples table...
Populating samples table...
Writing genes table
Reshaping geneData table
Recasting
Writing geneData table
Reading cuffdata_120417/gene_exp.diff
Error in function (classes, fdef, mtable)  : 
  unable to find an inherited method for function "make.db.names", for signature "SQLiteConnection", "logical"
>
IMO there should be something wrong(format?) in my gene_exp.diff so the RSQLite package aborted. And the cuffData.db do built up but I'm wondering if it is complete..
Hope for your reply. Thanks ^_^
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Old 04-17-2012, 06:02 PM   #2
lgoff
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Please make sure that your sample names are unique and do not have funky characters or begin with numeric values.

Feel free to contact me directly if you continue to have problems.

Cheers,
Loyal
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Old 04-18-2012, 11:49 PM   #3
dadada4ever
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Location: Beijing

Join Date: Mar 2010
Posts: 18
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Problem solved.

The reason why cummeRbund stuck is I use the sample name as "T" and R think the T is a logical value "True". When i changed the sample name then the problem solved.

Thank for Loyal and hope this (stupid unique) question may helpful to others.
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Old 07-31-2013, 10:13 AM   #4
jp.
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Talking

Hi there ?
I have the same problem and did the same mistake; trying again with new sample name and will let you know if this sort out the problem.
Thank you

Quote:
Originally Posted by lgoff View Post
Please make sure that your sample names are unique and do not have funky characters or begin with numeric values.

Feel free to contact me directly if you continue to have problems.

Cheers,
Loyal
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