Question: Some problems about cummeRbund running
1
gravatar for Ginsea Chen
5.4 years ago by
Ginsea Chen130
Chinese Academy of Tropical Agricultural Sciences, Danzhou, China
Ginsea Chen130 wrote:

Hi

There were some problems when I use cummeRbund to create a cummeRbund database from the cuffdiff output. My operation as follows:

> library(cummeRbund)
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: ‘BiocGenerics’

The following objects are masked from ‘package:parallel’:

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following object is masked from ‘package:stats’:

    xtabs

The following objects are masked from ‘package:base’:

    anyDuplicated, append, as.data.frame, as.vector, cbind, colnames,
    do.call, duplicated, eval, evalq, Filter, Find, get, intersect,
    is.unsorted, lapply, Map, mapply, match, mget, order, paste, pmax,
    pmax.int, pmin, pmin.int, Position, rank, rbind, Reduce, rep.int,
    rownames, sapply, setdiff, sort, table, tapply, union, unique,
    unlist

Loading required package: RSQLite
Loading required package: DBI
Loading required package: ggplot2
Need help? Try the ggplot2 mailing list: http://groups.google.com/group/ggplot2.
Loading required package: reshape2
Loading required package: fastcluster

Attaching package: ‘fastcluster’

The following object is masked from ‘package:stats’:

    hclust

Loading required package: rtracklayer
Loading required package: GenomicRanges
Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: Gviz
Loading required package: grid

Attaching package: ‘cummeRbund’

The following object is masked from ‘package:GenomicRanges’:

    promoters

The following object is masked from ‘package:IRanges’:

    promoters

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

I don't know how to solve the error message, so I ask for your help.

rna-seq cummerbund R • 3.2k views
ADD COMMENTlink written 5.4 years ago by Ginsea Chen130

I remember a SeqAnswers thread last year with some people having this issue.   Here it is: http://seqanswers.com/forums/showthread.php?t=19402

ADD REPLYlink modified 5.4 years ago • written 5.4 years ago by Alastair Kerr5.2k

Thanks for your help!

ADD REPLYlink written 5.4 years ago by Ginsea Chen130

Did you solve the problem? I am having the same one and can't find a way to solve it on my on.

ADD REPLYlink written 3.2 years ago by juafonso_bio40
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