Errors in cummerbund database creation and geneset formation
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5.9 years ago

Hello everyone, I am new to R and cummeRbund, but I would like to share with you some problems 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/ Writing runInfo Table Reading Read Group Info /home/alessio/R/i686-pc-linux-gnu-library/3.2/ Writing replicates Table Reading Var Model Info /home/alessio/R/i686-pc-linux-gnu-library/3.2/ 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

Another one is when i Try to build a geneset,this is my error code:

data(sampleData) > myGeneIds<-sampleIDs > myGeneIds [1] "XLOC_001363" "XLOC_001297" "XLOC_001339" "XLOC_000132" "XLOC_001265" [6] "XLOC_000151" "XLOC_001359" "XLOC_000069" "XLOC_000170" "XLOC_000105" [11] "XLOC_001262" "XLOC_001348" "XLOC_001411" "XLOC_001369" "XLOC_000158" [16] "XLOC_001370" "XLOC_001263" "XLOC_000115" "XLOC_000089" "XLOC_001240" > myGenes<-getGenes(cuff,myGeneIds) Getting gene information: FPKM Error in sqliteSendQuery(con, statement, : error in statement: near ")": syntax error

Sorry for the long Thread but I would like really to solve this problem thanks to you. Thank you in advance

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