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  • Error in CummeRbund

    Hi everyone,

    I am new to R and cummeRbund, but I would like to share with you a problem that occurred to me.

    I'm tryin to build a cufflinks database to analyze which genes are more expressed in IPSc VS normal cells,and I put in my working directory all the files that the company who did the run sent me.

    First question that I wanted to ask you: which KInd of files I have to put inside the dir? I mean I have two folders:cufflinks and cuff diff,Inside of cufflinks there are 3 files: genes.fpkm_tracking,isoforms.fpkm_tracking,transcripts.gtf and in the cuffdiff there another file called genes.fpkm_tracking and isoforms.fpkm,which one i have to put inside the working directory?

    Second question: when I try to build the cuffdata.db this the error that comes out:
    cuff<-readCufflinks(genome="Hg38",gtfFile="transcripts.gtf",rebuild=T)
    Creating database /home/alessio/R/i686-pc-linux-gnu-library/3.2/cuffData.db
    Reading Run Info File /home/alessio/R/i686-pc-linux-gnu-library/3.2/run.info
    Writing runInfo Table
    Reading Read Group Info /home/alessio/R/i686-pc-linux-gnu-library/3.2/read_groups.info
    Writing replicates Table
    Reading Var Model Info /home/alessio/R/i686-pc-linux-gnu-library/3.2/var_model.info
    Writing varModel Table
    Reading GTF file
    Writing GTF features to 'features' table...
    Reading /home/alessio/R/i686-pc-linux-gnu-library/3.2/genes.fpkm_tracking
    Checking samples table...
    Populating samples table...
    Writing genes table
    Reshaping geneData table
    Recasting
    Writing geneData table
    Reading /home/alessio/R/i686-pc-linux-gnu-library/3.2/gene_exp.diff
    Error in (function (classes, fdef, mtable) :
    unable to find an inherited method for function ‘make.db.names’ for signature ‘"SQLiteConnection", "integer"’
    Inoltre: Warning message:
    attributes are not identical across measure variables; they will be dropped

    These are my session INfos:
    R version 3.2.3 (2015-12-10)
    Platform: i686-pc-linux-gnu (32-bit)
    Running under: Ubuntu 14.04.3 LTS

    locale:
    [1] LC_CTYPE=it_IT.UTF-8 LC_NUMERIC=C
    [3] LC_TIME=it_IT.UTF-8 LC_COLLATE=it_IT.UTF-8
    [5] LC_MONETARY=it_IT.UTF-8 LC_MESSAGES=it_IT.UTF-8
    [7] LC_PAPER=it_IT.UTF-8 LC_NAME=C
    [9] LC_ADDRESS=C LC_TELEPHONE=C
    [11] LC_MEASUREMENT=it_IT.UTF-8 LC_IDENTIFICATION=C

    attached base packages:
    [1] grid stats4 parallel stats graphics grDevices utils
    [8] datasets methods base

    other attached packages:
    [1] cummeRbund_2.12.0 Gviz_1.14.0 rtracklayer_1.30.1
    [4] GenomicRanges_1.22.2 GenomeInfoDb_1.6.1 IRanges_2.4.6
    [7] S4Vectors_0.8.5 fastcluster_1.1.16 reshape2_1.4.1
    [10] ggplot2_2.0.0 RSQLite_1.0.0 DBI_0.3.1
    [13] BiocGenerics_0.16.1

    loaded via a namespace (and not attached):
    [1] Formula_1.2-1 futile.options_1.0.0
    [3] Rsamtools_1.22.0 zlibbioc_1.16.0
    [5] bitops_1.0-6 SummarizedExperiment_1.0.1
    [7] lattice_0.20-33 foreign_0.8-66
    [9] stringr_1.0.0 GenomicAlignments_1.6.1
    [11] dichromat_2.0-0 biomaRt_2.26.1
    [13] BSgenome_1.38.0 Biobase_2.30.0
    [15] biovizBase_1.18.0 Rcpp_0.12.2
    [17] gridExtra_2.0.0 plyr_1.8.3
    [19] tools_3.2.3 RCurl_1.95-4.7
    [21] BiocParallel_1.4.3 VariantAnnotation_1.16.4
    [23] lambda.r_1.1.7 XVector_0.10.0
    [25] futile.logger_1.4.1 scales_0.3.0
    [27] nnet_7.3-11 digest_0.6.8
    [29] gtable_0.1.2 stringi_1.0-1
    [31] latticeExtra_0.6-26 cluster_2.0.3
    [33] rpart_4.1-10 munsell_0.4.2
    [35] XML_3.98-1.3 colorspace_1.2-6
    [37] AnnotationDbi_1.32.3 magrittr_1.5
    [39] Hmisc_3.17-1 splines_3.2.3
    [41] Biostrings_2.38.2 survival_2.38-3
    [43] RColorBrewer_1.1-2 GenomicFeatures_1.22.7
    [45] acepack_1.3-3.3 matrixStats_0.50.1

    Sorry for the long Thread but I've looked for the answer in a lot of forums but anyone got the right one. I would like really to solve this problem thanks to you.

    Thank you in advance
    Last edited by gasteropode; 12-31-2015, 01:48 AM.

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