cummeRbound problem when reading cuffdiff output
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ds920207 • 0
@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.

software error R differential gene expression • 745 views
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