Errors in cummerbund database creation and geneset formation
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6.6 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 trying 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

This is my session Info:

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, bind.data) : 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

RNA-Seq R cummerbund • 2.0k views
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