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ds920207
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@ds920207-13406
Last seen 6.8 years ago
I recently started working with RNA-Seq analyse and I reached the step where I analyze my data using cummeRbund in R.but when I run readCufflinks ,I got an error :Column name mismatch.
> cuff_data<-readCufflinks('cuffdiff') Creating database cuffdiff/cuffData.db Reading Run Info File cuffdiff/run.info Writing runInfo Table Reading Read Group Info cuffdiff/read_groups.info Writing replicates Table Reading Var Model Info cuffdiff/var_model.info Writing varModel Table Reading cuffdiff/genes.fpkm_tracking Checking samples table... Populating samples table... Error: Column name mismatch. In addition: There were 50 or more warnings (use warnings() to see the first 50) > sessionInfo()
here it is my sessionInfo()
R version 3.4.1 (2017-06-30) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu 14.04.5 LTS Matrix products: default BLAS: /usr/lib/libblas/libblas.so.3.0 LAPACK: /usr/lib/lapack/liblapack.so.3.0 locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 LC_PAPER=en_US.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] grid stats4 parallel stats graphics grDevices utils datasets methods base other attached packages: [1] DBI_0.7 cummeRbund_2.18.0 Gviz_1.20.0 rtracklayer_1.36.3 GenomicRanges_1.28.3 GenomeInfoDb_1.12.2 [7] IRanges_2.10.2 S4Vectors_0.14.3 fastcluster_1.1.22 reshape2_1.4.2 ggplot2_2.2.1 RSQLite_2.0 [13] BiocGenerics_0.22.0 loaded via a namespace (and not attached): [1] httr_1.2.1 Biobase_2.36.2 AnnotationHub_2.8.2 bit64_0.9-7 [5] splines_3.4.1 shiny_1.0.3 Formula_1.2-1 interactiveDisplayBase_1.14.0 [9] latticeExtra_0.6-28 blob_1.1.0 BSgenome_1.44.0 GenomeInfoDbData_0.99.0 [13] Rsamtools_1.28.0 yaml_2.1.14 backports_1.1.0 lattice_0.20-35 [17] biovizBase_1.24.0 digest_0.6.12 RColorBrewer_1.1-2 XVector_0.16.0 [21] checkmate_1.8.2 colorspace_1.3-2 httpuv_1.3.3 htmltools_0.3.6 [25] Matrix_1.2-10 plyr_1.8.4 pkgconfig_2.0.1 XML_3.98-1.9 [29] biomaRt_2.32.1 zlibbioc_1.22.0 xtable_1.8-2 scales_0.4.1 [33] BiocParallel_1.10.1 htmlTable_1.9 tibble_1.3.3 AnnotationFilter_1.0.0 [37] SummarizedExperiment_1.6.3 GenomicFeatures_1.28.4 nnet_7.3-12 lazyeval_0.2.0 [41] mime_0.5 survival_2.41-3 magrittr_1.5 memoise_1.1.0 [45] foreign_0.8-69 BiocInstaller_1.26.0 tools_3.4.1 data.table_1.10.4 [49] matrixStats_0.52.2 stringr_1.2.0 munsell_0.4.3 cluster_2.0.6 [53] DelayedArray_0.2.7 AnnotationDbi_1.38.1 ensembldb_2.0.3 Biostrings_2.44.1 [57] compiler_3.4.1 rlang_0.1.1 RCurl_1.95-4.8 dichromat_2.0-0 [61] VariantAnnotation_1.22.3 htmlwidgets_0.8 bitops_1.0-6 base64enc_0.1-3 [65] gtable_0.2.0 curl_2.7 R6_2.2.2 GenomicAlignments_1.12.1 [69] gridExtra_2.2.1 knitr_1.16 bit_1.1-12 Hmisc_4.0-3 [73] ProtGenerics_1.8.0 stringi_1.1.5 Rcpp_0.12.11 rpart_4.1-11 [77] acepack_1.4.1
my sample name are h1_1_1/_2,h1_EPS_1_1 /-2,ES1_EPS_1/_1.
how to solve the problem ?
Any help will be appreciated.