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  • Gonza
    replied
    Hey ramma, did you figure that out? i m stuck in the same place....
    thanks
    G

    Leave a comment:


  • Ntobe
    replied
    Hi

    I have been trying to use my CummeRbund and it keep giving me the same error. I removed the cuffData.db from my working directory but it didn't help.

    > myGenes<-getGenes(cuff,myGeneIds)
    Getting gene information:
    FPKM
    Error in sqliteExecStatement(con, statement, bind.data) :
    RS-DBI driver: (error in statement: near ")": syntax error)

    Can anyone please help, I'm stuck.

    Nonto

    Leave a comment:


  • gwilymh
    replied
    I have had the same error and not been able to resolve it:

    Input:
    geneList<-as.vector(read.table("genesofInterest.txt",sep = "\t",header= FALSE),mode="list")
    geneList
    geneExp<-getGenes(cuff,geneList)
    Output:
    Getting gene information:
    FPKM
    Error in sqliteExecStatement(con, statement, bind.data) :
    RS-DBI driver: (error in statement: near ")": syntax error)

    I am working with CummeRbund version 2.0, and (I think) the CuffDiff data was generated with Cufflinks 2.0.2.

    I have tried clearing the workspace and reconnecting with CummeRbund; re-downloading all the CuffDiff output files and rebuilding the cuffData.db database; but I still get the same error.

    CummeRbund was working fine a few weeks ago with these commands, then abruptly started producing this error message.

    Has anyone found away around this problem?


    Originally posted by wacguy View Post
    Hi all,

    Quite some errors in CummeRbund; here is the list including the sessionInfo() at the end. I've been trying to solve these isuues for the last 2-3 weeks with little success. Some features worked on our server, quite some more when I ran it on my computer (mac 10.6.8), but still a lot of errors which are very cryptic to me: not a programmer/R master; just learn all Bowtie/tophat/cuff*...

    > myGenes<-getGenes(cuff,myGeneIds)
    Getting gene information:
    FPKM
    Error in sqliteExecStatement(con, statement, bind.data) :
    RS-DBI driver: (error in statement: near ")": syntax error)


    > genes.MDS<-MDSplot(genes(cuff))#sthash.hkJEYpTT.dpuf
    Error in cmdscale(d, eig = TRUE, k = 2) :
    'k' must be in {1, 2, .. n - 1}

    ic<-csCluster(myGenes,k=4)
    Error in csCluster(myGenes, k = 4) :
    error in evaluating the argument 'object' in selecting a method for function 'csCluster': Error: object 'myGenes' not found

    mySimilar<-findSimilar(cuff,"PINK1",n=20)
    Error in sqliteExecStatement(conn, statement, ...) :
    RS-DBI driver: (RS_SQLite_exec: could not execute1: cannot start a transaction within a transaction)

    mySimilar2<-findSimilar(cuff,myProfile,n=10)
    Error in sqliteExecStatement(conn, statement, ...) :
    RS-DBI driver: (RS_SQLite_exec: could not execute1: cannot start a transaction within a transaction)
    In addition: There were 50 or more warnings (use warnings() to see the first 50)



    > sessionInfo()
    R version 3.0.1 (2013-05-16)
    Platform: x86_64-apple-darwin10.8.0 (64-bit)

    locale:
    [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

    attached base packages:
    [1] grid parallel stats graphics grDevices utils datasets
    [8] methods base

    other attached packages:
    [1] cummeRbund_2.2.0 Gviz_1.4.4 rtracklayer_1.20.4
    [4] GenomicRanges_1.12.4 IRanges_1.18.2 fastcluster_1.1.11
    [7] reshape2_1.2.2 ggplot2_0.9.3.1 RSQLite_0.11.4
    [10] DBI_0.2-7 BiocGenerics_0.6.0

    loaded via a namespace (and not attached):
    [1] AnnotationDbi_1.22.6 Biobase_2.20.1 biomaRt_2.16.0
    [4] Biostrings_2.28.0 biovizBase_1.8.1 bitops_1.0-5
    [7] BSgenome_1.28.0 cluster_1.14.4 colorspace_1.2-2
    [10] dichromat_2.0-0 digest_0.6.3 GenomicFeatures_1.12.3
    [13] gtable_0.1.2 Hmisc_3.12-2 labeling_0.2
    [16] lattice_0.20-15 MASS_7.3-28 munsell_0.4.2
    [19] plyr_1.8 proto_0.3-10 RColorBrewer_1.0-5
    [22] RCurl_1.95-4.1 rpart_4.1-1 Rsamtools_1.12.3
    [25] scales_0.2.3 stats4_3.0.1 stringr_0.6.2
    [28] tools_3.0.1 XML_3.95-0.2 zlibbioc_1.6.0

    Help would be highly appreciate; Thanks a lot,
    Guy

    Leave a comment:


  • IBseq
    replied
    dear all,
    any suggestion more than wellcome!

    <environment: namespace:cummeRbund>
    > cuff<-readCufflinks(rebuild=T)
    Creating database /home/bsib/Cuffdiff/caski/cuffData.db
    Reading /home/bsib/Cuffdiff/caski/genes.fpkm_tracking
    Checking samples table...
    Populating samples table...
    Writing genes table
    Reshaping geneData table
    Recasting
    Writing geneData table
    Reading /home/bsib/Cuffdiff/caski/gene_exp.diff
    Writing geneExpDiffData table
    Reading /home/bsib/Cuffdiff/caski/promoters.diff
    Writing promoterDiffData table
    Reading /home/bsib/Cuffdiff/caski/isoforms.fpkm_tracking
    Checking samples table...
    OK!
    Writing isoforms table
    Reshaping isoformData table
    Recasting
    Writing isoformData table
    Reading /home/bsib/Cuffdiff/caski/isoform_exp.diff
    Writing isoformExpDiffData table
    Reading /home/bsib/Cuffdiff/caski/tss_groups.fpkm_tracking
    Checking samples table...
    OK!
    Writing TSS table
    Reshaping TSSData table
    Recasting
    Writing TSSData table
    Reading /home/bsib/Cuffdiff/caski/tss_group_exp.diff
    Writing TSSExpDiffData table
    Reading /home/bsib/Cuffdiff/caski/splicing.diff
    Writing splicingDiffData table
    Reading /home/bsib/Cuffdiff/caski/cds.fpkm_tracking
    Checking samples table...
    OK!
    Writing CDS table
    Reshaping CDSData table
    Recasting
    Writing CDSData table
    Reading /home/bsib/Cuffdiff/caski/cds_exp.diff
    Writing CDSExpDiffData table
    Indexing Tables...
    > d<-dispersionPLot(genes(cuff))
    Error: could not find function "dispersionPLot"
    >


    thanks a lot!

    Leave a comment:


  • IBseq
    replied
    im new to r btwa
    abd unix/linux as well...

    gosh!helpppp!

    Leave a comment:


  • IBseq
    replied
    Hi,
    I have human cervical samples. No replicates. this one i posted is one of the samples I have compared with the negative sample...

    i'm struggling writing down commands...! I need to create a gene set I have to work with out of all those that came from the sequencing. How can I do that??

    Any help much appreciated!
    ibseq

    Leave a comment:


  • wacguy
    replied
    can you give us a bit more info

    which organism, how many samples and replicas, the commands and errors messages. Are you familiar with R?

    Guy

    Leave a comment:


  • IBseq
    replied
    hi,
    can anyone help me out with this?
    > library(cummeRbund)
    Loading required package: RSQLite
    Loading required package: DBI
    Loading required package: ggplot2
    Loading required package: reshape2
    > cuff <- readCufflinks()
    > cuff
    CuffSet instance with:
    2 samples
    24300 genes
    42209 isoforms
    28820 TSS
    25042 CDS
    24300 promoters
    28820 splicing
    0 relCDS


    why us relCDS 0?

    Also, when I try to use many function of cummerbund such as cs Boxplot, cs Dendro and many others I have a error message and thus I cannot build up the pic or graph, its like I do not have that function..

    any suggestion will be much appreciated!

    ibseq

    Leave a comment:


  • wacguy
    replied
    Hi all,

    Quite some errors in CummeRbund; here is the list including the sessionInfo() at the end. I've been trying to solve these isuues for the last 2-3 weeks with little success. Some features worked on our server, quite some more when I ran it on my computer (mac 10.6.8), but still a lot of errors which are very cryptic to me: not a programmer/R master; just learn all Bowtie/tophat/cuff*...

    > myGenes<-getGenes(cuff,myGeneIds)
    Getting gene information:
    FPKM
    Error in sqliteExecStatement(con, statement, bind.data) :
    RS-DBI driver: (error in statement: near ")": syntax error)


    > genes.MDS<-MDSplot(genes(cuff))#sthash.hkJEYpTT.dpuf
    Error in cmdscale(d, eig = TRUE, k = 2) :
    'k' must be in {1, 2, .. n - 1}

    ic<-csCluster(myGenes,k=4)
    Error in csCluster(myGenes, k = 4) :
    error in evaluating the argument 'object' in selecting a method for function 'csCluster': Error: object 'myGenes' not found

    mySimilar<-findSimilar(cuff,"PINK1",n=20)
    Error in sqliteExecStatement(conn, statement, ...) :
    RS-DBI driver: (RS_SQLite_exec: could not execute1: cannot start a transaction within a transaction)

    mySimilar2<-findSimilar(cuff,myProfile,n=10)
    Error in sqliteExecStatement(conn, statement, ...) :
    RS-DBI driver: (RS_SQLite_exec: could not execute1: cannot start a transaction within a transaction)
    In addition: There were 50 or more warnings (use warnings() to see the first 50)



    > sessionInfo()
    R version 3.0.1 (2013-05-16)
    Platform: x86_64-apple-darwin10.8.0 (64-bit)

    locale:
    [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

    attached base packages:
    [1] grid parallel stats graphics grDevices utils datasets
    [8] methods base

    other attached packages:
    [1] cummeRbund_2.2.0 Gviz_1.4.4 rtracklayer_1.20.4
    [4] GenomicRanges_1.12.4 IRanges_1.18.2 fastcluster_1.1.11
    [7] reshape2_1.2.2 ggplot2_0.9.3.1 RSQLite_0.11.4
    [10] DBI_0.2-7 BiocGenerics_0.6.0

    loaded via a namespace (and not attached):
    [1] AnnotationDbi_1.22.6 Biobase_2.20.1 biomaRt_2.16.0
    [4] Biostrings_2.28.0 biovizBase_1.8.1 bitops_1.0-5
    [7] BSgenome_1.28.0 cluster_1.14.4 colorspace_1.2-2
    [10] dichromat_2.0-0 digest_0.6.3 GenomicFeatures_1.12.3
    [13] gtable_0.1.2 Hmisc_3.12-2 labeling_0.2
    [16] lattice_0.20-15 MASS_7.3-28 munsell_0.4.2
    [19] plyr_1.8 proto_0.3-10 RColorBrewer_1.0-5
    [22] RCurl_1.95-4.1 rpart_4.1-1 Rsamtools_1.12.3
    [25] scales_0.2.3 stats4_3.0.1 stringr_0.6.2
    [28] tools_3.0.1 XML_3.95-0.2 zlibbioc_1.6.0

    Help would be highly appreciate; Thanks a lot,
    Guy

    Leave a comment:


  • Charitra
    replied
    Originally posted by shabhonam View Post
    Hello Charita,

    I had the similar problem, try to remove all the # from gene names from the genes.fpkmtracking or any other file which shows error. Always remove the cuffData.db from your working directory before rerunning the commands:
    library(cummeRbund)
    cuff <- readCufflinks()

    Cheers
    Shab
    Dear shabhonam
    I got another problem with cuffdiff or cummeRbund.
    in R cummeRbund, it can not find gene but gene is there in my cuffdiff output when I checked manually ... is this errog in cuffdiff or cummeRbund ??

    Leave a comment:


  • Charitra
    replied
    Thank you so much for your kind help.
    Now its going smooth.
    O\One more thing, can you tell me something about how to do pathway analysis after differential expression (cuffdiff).

    Charitra

    Leave a comment:


  • shabhonam
    replied
    Hello Charita,

    I had the similar problem, try to remove all the # from gene names from the genes.fpkmtracking or any other file which shows error. Always remove the cuffData.db from your working directory before rerunning the commands:
    library(cummeRbund)
    cuff <- readCufflinks()

    Cheers
    Shab

    Leave a comment:


  • Charitra
    replied
    I have the same problem, what is the solution ???

    cuff_data <- readCufflinks('diff_out')
    Creating database diff_out/cuffData.db
    Error in sqliteNewConnection(drv, ...) :
    RS-DBI driver: (could not connect to dbname:
    unable to open database file


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

    Leave a comment:


  • billstevens
    replied
    Sorry, this is actually a really silly mistake. My working directory was diff_out, not the folder that points to diff_out.

    Leave a comment:


  • billstevens
    replied
    Hi guys, I'm working with the CummeRbund package. I have used the package before and have found it to be very useful. I just upgraded to the new cufflinks package (2.0.1), but when I run use CummeRbund to analyze my cuffdiff output, I receive the following error:


    > cuffy <- readCufflinks('diff_out')
    Creating database diff_out/cuffData.db
    Error in sqliteNewConnection(drv, ...) :
    RS-DBI driver: (could not connect to dbname:
    unable to open database file
    )

    I re-ran this on a 'diff_out' folder that I've used previously with success (version 1.3), and I received the same error. I noticed someone else in a different forum had the same issue. Do you guys have any idea what's going on? Its the first step, I just run "library(cummeRbund)" and then this command, but somehow, it won't work. I'm using cummeRbund 1.2 and R 2.15.

    Leave a comment:

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